Where are the relics of Anthony the Great?

In reality this is much disputed, although each theory is 'the only true one.'

We see traditions for: his original unknown grave, a tomb below a monastery in Egypt, remaining in Alexandria, remaining in Constantinople, and in relic sites in France, of which alone there are three Saint-Antoine-L’Abbaye, Lézat, and Arles. Added to that we see a lot of smaller particles scattered all around geographically revered as 'true relics'.

'Naturally', the first option of secrecy remains entirely one of belief and conviction. All the smaller parts that are claimed to be part of his remains likewise. The two options St-Antoine and Arles do show bones to the public.

So, from a historians view point, we do not know for sure. His two disciples kept the whereabouts of his remains secret.
From a believer's point of view it is 'choose your affiliation'. But the question asks for a 'better sources' and more than 'half of the story'.

The overwhelming number of Catholic sources just tell the story that the 'relics are in Arles', where the church St-Julien holding them most of the time was previously called 'St-Antoine'.

The relics are said to have been indeed not kept in one package, but the main stash is still kept in Arles:

Anthony's veneration began as early as the 5th century. His relics were transferred to Alexandria in 561 after the discovery of his alleged tomb, and in 635 - after the conquest of Egypt by the Muslims - they came to Constantinople - today's Ístanbul, then around 1000 the greater part of them came to southern France to the monastic church in St-Didier-de-la-Tour; these were taken to the church of St-Julien in Arles in 1491, and since its profanation after destruction by German bombs in 1944 they have been in the city's cathedral.

Relics also arrived in the Dauphiné around 1074; these were taken to La-Motte-aux-Bois in 1089, where the ancestral monastery of the Antonite Order was founded; in 1083 the place was therefore renamed St-Antoine-l'Abbaye. Matthias Grünewald later created his Isenheim Altar for the Antonites.

Perhaps of interest, some dates around this:

Catholic day of remembrance: 17 January, Mandatory day of remembrance, Not observed day of remembrance in the Mozarabic rite, Solemnity in Menorca, Commemoration day III. class

• Transfer of remains to Arles: 9 January

• Transfer of the bones: 15 February

• Transfer of the bones to the monastery of St-Antoine-l'Abbaye: 17 March

• Transfer of the bones from Constantinople to the monastery of St-Antoine-l'Abbaye: 11 May

• Third reception of the bones in St-Didier-de-la-Tour: 3 June

• Transfer of the bones to Lézat-sur-Lèze near Toulouse: 9 June in the monastery of St Anthony in Paris and in the monastery of Lubeca near Noyon: 10 June

• Discovery of the bones: 11 June

• Transfer of the bones to Constantinople: 12 June

• Transfer of the bones revealed by Gabriel to Vienne: 13 June

— Joachim Schäfer: Artikel "Antonius „der Große”", aus dem Ökumenischen Heiligenlexikon - https://www.heiligenlexikon.de/BiographienA/Antonius_der_Grosse.htm, visited 2021 (translated)

This mirrors the information found in

His grave is said to have been discovered in 561. His bones were transferred to Alexandria, from where they were brought to Egypt in 635, after the conquest of Egypt by the Muslims. Constantinople. Around 1000, the greater part of the relics came to France to the priory church of St-Didier de la Motte (Diocese of Vienne) and finally to their present resting place in the parish church of St-Julien in Arles in 1491.

— Michael Buchberger & Walter Kasper (eds): "Lexikon für Theologie und Kirche (LThK3)" Vol 1, Herder, Freiburg, 1993. (p787, translated)

In conclusion it seems that the main confusion stems from the misreading of the French diocese 'Vienne' as "Vienna" in Austria, and that the relics and that the church holding the relics initially was later renamed from 'St-Antoine' to 'St-Julien'. That yet later the relics remained in Arles but were transferred to the main (now former) cathedral 'St-Trophime':

Chapelles :

D- saint Antoine de Padoue, E- saint Joseph ou des âmes du Purgatoire, F- saint Genès, G- Sainte Croix, H- saint Antoine du Désert, I- des reliques

'Antoine du Désert' is Anthony the Great.

— Steve Grant: "Relics of St Anthony of the desert"
This reliquary holds the skull and a leg bone of St Anthony of the desert. It is in the church of St Trophime in Arles, France

That is the most popular 'official' story.

The 'more complete version of this story' is apparently a bit more complex:

Reliquary of Saint Anthony (gold, 19th century) exhibited in the church of Saint-Trophime since 1999.

In the face of Saracen expansion, his body was transferred to Saint Sophia in Constantinople around the year 670; it rested there until the 11th century, when it was transported to Europe by a Dauphin baron, Jocelin. The Benedictines of Montmajour took possession of it in 1083, when the church of Saint-Antoine in Isère was given to the Abbey of Montmajour in Arles.

At the same time as the Benedictine establishment, and faced with the development of ergotism (a kind of gangrene caused by a fungus that develops on spoiled grain, particularly rye), a hospital order appeared: the Brothers of Alms or Antonines.

A rivalry arose between the two orders, leading to the expulsion of the Benedictines by the Antonines in 1290: fere midi ignominiose fuerunt expulsi. This act marked the origin of the antagonism between Arles and Saint-Antoine in Isère over the possession of the relics of Saint-Antoine abbot. Indeed, if until then the relics had remained in Dauphiné, under the custody of the two orders (the Antonines held one arm, and the Benedictines the rest of the body), after 1290 opinions diverged.

The Benedictines claimed to have taken with them the part of the relics in their custody, while the Antonines claimed that they left it behind.

At first, this debate was overshadowed by that of the compensation owed by the Hospitallers (transformed into a regular order) to the Benedictines for the loss of the priory of Saint-Antoine (erected into an abbey). An annual pension of 1,300 livres tournois was thus attributed in perpetuity to Montmajour.

This continued for two hundred years, until June 1490, when a papal bull reversed the situation by placing the Arles abbey under the domination of the Dauphin abbey, thereby abolishing the pension. The affair lasted until 31 December 1495, when a bull from Alexander VI abolished the union of the two abbeys.

It was in this troubled context that the relics became a political issue and that the quarrel over the legitimacy of their possession was revived. Although their presence at the Benedictine abbey of Arles is attested only by very rare writings, it seems to be confirmed by the discovery of lead pilgrimage badges around Montmajour. Their presence hardly seems to be explained outside the context of a pilgrimage.

Fearing an attempt by the Antonines to take possession of the Arles abbey, the relics were solemnly transferred to Saint-Julien d'Arles on Sunday 9 January 1491 (1490 if the date is correct). January 1491 (1490 if one considers the calendar style of the Annunciation).

Under this translation, the church of Saint-Julien was placed under the double vocative Saint-Julien/Saint-Antoine, and Saint Antoine abbot, considered with Saint Mark, as one of the patrons of the city was the object of an important devotion.

His statue adorned one of the towers of the cavalry gate, and his procession was the most important, since it regulated the route of the other Arles processions every year.

Her silver reliquary bust, which was one of the most important in Arles, after having escaped the silver smelting of the 18th century, fell victim to the crucible into which the Revolution threw so many works of art. His relics were restored to worship by decision of the Congregation of Rites in 1859 after many ups and downs which saw the debate on their authenticity between Arles and Saint-Antoine l'abbaye revive.

The oblivion into which the devotion to Saint Anthony abbot has been plunged for half a century in Arles contrasts singularly with the fervour it arouses in the Christian world, both Roman and Orthodox. Thus, the Arles relics are more adored in Italy, where the hunt is regularly sent, than in Arles itself. Let us hope that in the future the feast of Saint Anthony will once again become a highlight of the Arles liturgical year and that his hunt will be restored to the church that has housed it for over five hundred years.

— Arles Et Les Reliques De Saint Antoine Du Désert. Posted On 21 March 2021.
Text by Michel Baudat, extracted from the bulletin n°1 of the Association les Amis de la Major et de Saint-Julien Saint-Antoine "Histoire, patrimoine et accueil" d'Arles of 6 January 2008. (translated, original PDF)

From this we conclude that 'the Antonine treasure' is the treasure of the Antonine abbey, but does not mean to include the relics, and thus, when Saint-Antoine-l'Abbaye was plundered by Hugenots or came into trouble during the revolution, the 'main body' of relics were already elsewhere. This of course assumes that indeed the Benedictines in Arles actually had the true remains. For St-Antoine itself the numerous attacks during the religious wars brought much suffering and decline, but within all the looting, plundering, burning and theft, the alleged remains of Anthony were apparently descrated, the shrine violated, but the relics remained each time in place. (— Victor Advielle: "Histoire de l'ordre hospitalier de Saint-Antoine de Viennois et de ses Commaderies et Prieuriès", Paris, 1883. gBooks)

Although it was stated explicitly in the question that 'the alleged relics' and not the 'true ones' are inquired about, this actually needs still some addressing.

Since there are really three traditions to consider, of which we saw two so far. The third is of course that Anthony's remains are — at least for the most parts — still were they have always been:

Anthony, abbot - January 17th
St Anthony (d. 356, Mt. Colzim, Egypt) (Relics: Zaafarana, Egypt; Saint-Antoine-l'Abbaye, France; Arles, France)

St Anthony requested to be buried secretly in an unmarked grave. Therefore, the exact location of his tomb is unknown. Nevertheless several traditions have arisen about his relics. One tradition holds that his tomb rests directly under St Anthony’s Monastery in Egypt which was built close to where St Anthony had lived as a hermit. A second tradition holds that his tomb was discovered and that some of these relics were transported to France.

Saint Anthony’s Monastery, Zaafarana, Egypt *The tomb of St Anthony is believed to rest under this monastery as noted above.

Saint-Antoine-l'Abbaye (Abbey of Saint Anthony), 38160 Saint-Antoine-l’Abbaye, France *This monastery is located west of the city of Grenoble, France *Relics of St Anthony are said to have been transferred here around the 11th century.

L’Eglise Saint-Trophime (Church of Saint Trophime) 12 Rue du Cloître, 13200 Arles, France *Some relics of St Anthony are also said to rest in this church.

Wikipedia articles around this issue, usually favouring one side without explanation:

• Hospital Brothers of Saint Anthony: conflict between Antonines and Benedictines mentioned, relics portrayed as complete in St-Antoine l'abbaye.

• Antoine le Grand: only Saint-Antoine-l'Abbaye

• Antonius der Große: only Arles for 'the relics'; but also:

  Particles of the relics are also found in Echternach, Cologne (arm and beard relic) and Florence, among others. The monks of the Antonius Monastery in Egypt, on the other hand, are convinced that the mortal remains of the saint are still there where he was originally buried.

  The 'among others' may also include Bergisch-Gladbach and Herkenrath.

• Ordre hospitalier de Saint-Antoine: only Saint-Antoine-l'Abbaye, with picture of the chest alleged to contain 'the' relics)

• Antoniter-Orden: mentions they had the relics…

• Hospital Brothers of Saint Anthony: quarrel mentioned and emphasis on 'the shrine' remaining under Antonine control.

• Saint-Antoine-l'Abbaye: only Saint-Antoine-l'Abbaye

• Abbaye_de_Saint-Antoine-l'Abbaye: mentions the quarrel over the relics and the result as:

  In 1293, the abbot of Montmajour asked the archbishop of Vienne to re-establish his abbey at Saint-Antoine. This expulsion gave rise to a quarrel over where the relics of Saint Anthony were to be found, in the abbey of Saint Anthony or in the church of Saint-Julien in Arles, where they were deposited on 9 January 1490 by the monks of Montmajour.

• Saint-Antoine-l’Abbaye: Benedictines were expelled and took the relics with them…

• Cathédrale Saint-Trophime_d'Arles: just mentions 'the relics'.

• Église Saint-Julien (Arles):

  The church was initially built in 1119. It belonged to the monks of Montmajour and was known at the time as the church of Saint-Antoine, whose relics had been kept in the abbey since 1491. […] Plundered during the Revolution, the church suffered even more from the Allied bombings of August 1944 which left it practically in ruins. Now restored, it is now closed to worship but is used as a hall for shows, concerts or exhibitions that are frequently held there.

• Antonius van Egypte: Dutch WP mentions the dispute over authenticity of the bones between St-Antoine and Arles, and even hints at the entire relic being lost except for "some particles", and yet that an arm was kept in Cologne, and another part in Warfhuizen. Alas, all unsourced, which is quite unfortunate. The cologne reliquary of his beard in St Kunibert, in close-up.

• …

However, a popular history book summarises the story as the Benedictines simply committing repeated 'fraud': just claiming they took the relics, without really doing so. The book claims that Rome intervened several times in favour of St-Antoine and against the Benedictines from Montmajour in Arles. Although the latter continued to present expert opinions to assert their claims for Arles. (— Bernd Ingmar Gutberlet: "Die 50 größten Lügen und Legenden der Weltgeschichte", Bastei Lübbe, 2007. (gBooks, p81–84)

The last claim is not sourced but seems to rest on — Adalbert Mischlewski: "Die Antoniusreliquien in Arles - eine auch heute noch wirksame Fälschung des 15. Jahrhunderts", in: "Fälschungen im Mittelalter Tl. 5 S. 417-431, Internationaler Kongreß der Monumenta Germaniae Historica München, 16.-19. September 1986 (Vol. 1-5), Monumenta Germaniae Historica. Schriften / 33, 1-5, - Hannover, 1988.

Which seems to cast pretty much doubt on the claims for the bones in Arles as derived from the ones of traditional belief in St-Antoine.

But this is all just based on contradictory information:

In spite of Athanasius’ insistence that the place of Anthony’s burial was known to only two of his disciples, the saint’s body was widely thought to have been moved out of Egypt before the Fall of Rome. A work of international notoriety, the anonymous De inventione corporis sancti Antonii, also known as the Legend of Theophilus, recounts the retrieval of Anthony’s relics from the Egyptian desert under the reign of the Emperor Constantine and their miraculous journey back to Constantinople.

This text, which explicitly acknowledges the Vita Antonii’s claim that Anthony’s place of burial was kept secret by his disciples, provided authorization to a medieval relic cult already well under way in the twelfth century.

By the time of the Vie de Saint Antoine’s composition, however, one iteration of Anthony’s post-mortem translation had attained special notoriety. The legendary foundation of this tradition is recounted in the anonymous Translacio sanctissimi confessoris Anthonii abbatis et heremite a Constantinopoli in Viennam, a continuation of the Legend of Theophilus which tells the story of a young nobleman by the name of Jacelin who retrieves Anthony’s relics from Constantinople and brings them home to the Dauphiné Viennois.

The relics remain in Jacelin’s family for generations until a papal decree obliges his descendants to give up the familial monopoly. At this point, one of Jacelin’s heirs, a certain Guigues, comes up with a plan to comply with the Pope’s wishes while keeping Anthony close at hand: he donates the relics to the Benedictines at Montmajour, about 120 miles south of his ancestral home, adding to this gift a parcel of his own land, a town in the Dauphiné Viennois which the author identifies as La Motte (Mota).

Here, a monastery is built to house Anthony’s remains and not far off, Guigues founds a hostel (‘domus helemosinaria’) where the poor and the sick can come to seek Anthony’s aid. This story, reasonably widespread from the thirteenth century onwards, provided the foundational narrative of what would grow to become one of the most vital pilgrimage sites in medieval France.

The arrival of Anthony’s relics in the Dauphiné Viennois, now typically dated to about 1070, was a major factor in the foundation of the Antonine order.

La Motte-Saint-Dider, the location identified by the author of the translation narrative as the site of Guigues’s donation, was subsequently renamed Saint- Antoine-L’Abbaye in honour of its new patron. Here, just as the Translacio describes it, a ‘domus helemosinaria’ took root under the direction of the Antonines, and rapidly built an international reputation following a particularly violent outbreak of ergotism at the end of the eleventh century.44 Ergotism, later known as ‘St Anthony’s Fire’, was a widespread and potentially fatal illness which, throughout the medieval period, afflicted its sufferers with a range of symptoms including painful burning, psychosis, and gangrene. In response to this and subsequent epidemics, the lay brothers of the nascent Antonine order devoted themselves to caring for the sick and, before long, cures thanks to their intervention began to draw pilgrims from all over Europe. This did not only make the shrine at Saint-Antoine-L’Abbaye into an important destination for pilgrims; it transformed Anthony’s cult into a relevant part of public health.

[…]

Although, as Fenelli points out, dating of this text is challenging (Dall’eremo alla stalla, p. 49), it was probably known throughout the high and late medieval periods, the earliest extant manuscript copy dating to the twelfth century (BnF, MS lat. 5579), and subsequent versions traced to the fifteenth and sixteenth. For more on the manuscript tradition and its translation into a variety of vernacular languages, see Fenelli, ‘Sant’Antonio Abate’, pp. 57–60. Although Fenelli signals the existence of one French-language rendering of this narrative (Los Angeles, J. Paul Getty Museum, MS Ludwig XI.8), it is worth noting that the collection of fifteenth-century manuscripts containing some version of this story in Old French is most likely significantly larger. A version of De inventione corporis sancti Antonii in Old French is available in Paris, Bibliothèque nationale de France, MS fr. 1882, fols 100r–147v. The same text has also been identified in at least one other coeval manuscript (Troyes, Bibliothèque Municipale, MS 0840). See Section romane, ‘notice’ de Translation de saint Antoine en Viennois dans la base Jonas-IRHT/CNRS http://jonas.irht.cnrs.fr/oeuvre/9639 (accessed 12 October 2017). Still another version appears in Paris, Bibliothèque nationale de France, MS fr. 987, fols 230r–236v. It is likely that this list is abbreviated. Just how abbreviated is difficult to say; the tradition of Anthony’s French-language translation accounts is in great need of more focused scholarly attention.

For acknowledgement of the Vita Antonii’s claim, see ‘De S. Anthonio Abbate ex codice Namurc. N. 159’, Analecta Bollandiana, 2 (1883), 341–54 (p. 342).

Aside from the three major relic sites in France (Saint-Antoine-L’Abbaye, Lézat, and Arles, which will be discussed in detail hereafter) a variety of viewpoints seem to have been held on Anthony’s remains.

As Alessandra Foscati demonstrates, for example, a robust high medieval tradition depicts Anthony’s translation to Alexandria ‘I tre corpi del santo: le leggende di traslazione delle spoglie di Sant’Antonio Abate in Occidente’, Hagiographica, 20 (2013), 143–81 (pp. 148f.)). Moreover, the belief that Anthony’s body might still be in Constantinople is represented in the sixteenth century by Jacques Meyer, in possible reference, Foscati hypothesizes, to an unknown medieval narrative (p. 174). ‘La Translation de Saint Antoine en Dauphiné’, ed. Paul Noordeloos, Analecta Bollandiana, 60 (1942), 68–81.

Noordeloos’s edition accounts for five discrete manuscripts (p. 72) but, as Fenelli points out, at least five others exist (‘Sant’Antonio Abate’, p. 80). It is this story, at least in its broad lines, that the first historian of the Antonine order, Aymarus Falco, would cite in his sixteenth-century Antoniæ historiæ compendium to justify the presence of Anthony’s relics in France (Lyon, 1533), fols 35v–38v.

For more specific comments on the relationship between the Translacio and Falco’s history, see Foscati, ‘I tre corpi del santo’, p. 165.

Adalbert Mischlewski, Un Ordre hospitalier au Moyen Âge: les chanoines réguliers de Saint-Antoine-en-Viennois, trans. Hermann and Denise Kuhn (Grenoble, 1995), pp. 12f.

— Christine Valerie Bourgeois: "Devotion And Disbelief In The Old French Vie De Saint Antoine", Medium Ævum, Vol. 87, No. 2, 2018, pp. 277–303 (jstor)

The three bodies of Anthony in France are thus:

Later in their travels, while staying at the Benedictine abbey of Saint-Pierre de Lézat (Lézat-sur-Léze, near Toulouse) at the foot of the Pyrenees, they wrote that they had seen a beautiful old cartularium which claimed that the abbey possessed (or believed to possess, as the fathers specified) the remains of Anthony the Abbot, which were still the object of a popular cult and were often used by the Toulouse parliament to take oaths.

The two Maurists were unable to hide their embarrassment, given that they had also witnessed the exposition of the remains of the same saint in Arles, in Provence, housed in an ‘impressive casket’ at Montmajour Abbey. The Benedictines there claimed to have appropriated them from the Antonines of Saint-Antoine ‘as something that belonged to them’. The authors duly stated that all this provided ‘the opportunity for critics to put their pens to use on such an interesting matter’.

An older account from the sixteenth century describes how Canon Antonio De Beatis was outraged by the fact that the saint had two bodies in Saint-Antoine and Arles. During his year-long trip (1517–1518) through Germany, France and the Low Countries with Cardinal Luigi d’Aragona he visited Arles immediately after Saint-Antoine and used the second saintly body as a pretext to criticise the existence of the identical relics he had seen displayed in various churches.

In his role as a representative of a modern Church which used stricter criteria to evaluate saintliness, he duly blamed the proliferation of relics on clergymen, accusing them of not carrying out authenticity checks.14 He admitted, however, that such procedures could no longer be imposed on the deeply rooted older cults, which had to be tolerated as ‘many cities, lands and peoples that have long-standing cults and possess old relics would rather be attacked and burnt a thousand times than be deprived of them’. Fortunately, after reaching the Côte d’Azur, Antonio de Beatis returned to Italy without visiting the Pyrenean foothills and was thus spared the further indignation he would have felt on finding Anthony’s third body in Lézat.

— Alessandra Foscati: "Saint Anthony’s Fire from Antiquity to the Eighteenth Century", Amsterdam University Press: Amsterdam, 2019, p129.