Did Northern troops attempt to re-enslave African Americans in Southern plantations during the Civil War?

From McPherson's Battle Cry of Freedom, p.711:

The need of northern and British textile mills for cotton also caused the army to put many freed people to work growing cotton—often on the same plantations where they had done the same work as slaves. Some of these plantations remained in government hands and were administered by "labor superintendents" sent by northern freedmen's aid societies. Others were leased to Yankee entrepreneurs who hoped to make big money raising cotton with free labor. Still others remained in the hands of their owners, who took the oath of allegiance and promised to pay wages to workers who had recently been their slaves. Some land was leased by the freedmen themselves, who farmed it without direct white supervision and in some cases cleared a handsome profit that enabled them subsequently to buy land of their own. The outstanding example of a self-governing black colony occurred at Davis Bend, Mississippi, where former slaves of the Confederate president and his brother leased their plantations (from the Union army, which had seized them) and made good crops.

The quality of supervision of contraband labor by northern superintendents, Yankee lessees, and southern planters ranged from a benign to a brutal paternalism, prefiguring the spectrum of labor relations after the war. Part of the freedmen's wages was often withheld until the end of the season to ensure that they stayed on the job, and most of the rest was deducted for food and shelter. Many contrabands, understandably, could see little difference between this system of "free" labor and the bondage they had endured all their lives. Nowhere was the apparent similarity greater than in occupied Louisiana, where many planters took the oath of allegiance and continued to raise cotton or sugar under regulations issued by General Banks. Because of the national political focus on the reconstruction process in Louisiana, these regulations became another irritant between radical and moderate Republicans and another issue in the controversy between Congress and president. By military fiat Banks fixed the wages for plantation laborers and promised that the army would enforce "just treatment, healthy rations, comfortable clothing, quarters, fuel, medical attendance, and instruction for children." But further regulations ensured that some of these promises were likely to be honored in the breach. A worker could not leave the plantation without a pass and must sign a contract to remain for the entire year with his employer, who could call on provost marshals to enforce "continuous and faithful service, respectful deportment, correct discipline and perfect subordination." This system amounted to a virtual "reestablishment of slavery," charged abolitionists. It "makes the [Emancipation] Proclamation of 1863 a mockery and delusion," said Frederick Douglass. "Any white man," declared the black newspaper in New Orleans, "subjected to such restrictive and humiliating prohibitions, would certainly call himself a slave." If "this is the definition [of freedom] which the administration and people prefer," observed a radical newspaper in Boston, "we have got to go through a longer and severer struggle than ever."

Question #1:
Did Northern troops attempt to re-enslave African Americans in Southern plantations during the Civil War?

Short Answer #1:
Not Just Northern Troops. It was the North's policy for the first year of the war, to be followed by all of it's generals. Generals who did not follow this policy (like John Fremont) and freed slaves risked losing their commands. While the South Fought the Civil war ultimately about slavery, or states right to keep slaves; the North reason for fighting was more nuanced. The North fought the civil war for many reasons and those reasons priorities changed over time. For the North it was initially about preserving the Union. For Abraham Lincoln the issue of slavery was a settled one. The civil war was fought to preserve the Union. Coincidentally under Lincoln's vision it was the preservation of the Union which would bring about the abolition of slavery. Early on in the American Civil War, Lincoln walked a delegate balance to entice the South back into the union peacefully, to stop border states from joining the Confederacy, and to motivate the Northern Free States to support him. As such one of Lincoln's political policies during this time was to preserve slavery in territories under Union Command.

Question #2:
Can someone recommend sources that describe these attempts, by the Union, to temporarily re-enslave the freed people on the very same plantations? How widespread was this and how did the North's military elites rationalize it?

Short Answer #2
With Regards to Nathanial Bank's actions in New Orleans 1863, you might read President Lincoln's letter to his friend Banks which dealt with Lincoln's ideas on what policy the General should be following. (see detailed answer be low.)

Detailed Answer #1 For Abraham Lincoln the American Civil war initially was not about Slavery because Slavery was to his mind a settled issue. The Slave holding south had lost the ability to spread the institution westward with the adoption of the Kansas Nebraska act which granted popular sovereignty to states entering the Union on the slavery issue. Before Kansas Nebraska all states entered the Union in pairs in order to preserve the delegate balance of power between slave and free states. After Kansas Nebraska the decision would be left to the local populations, which either originated in the more populous anti slavery North, or immigrated from anti slavery Europe, and with a Majority of manual laborers who saw slaves as economic competition for jobs. The South fought a decades long war in Kansas to get it to change it's position on slavery, ultimately failing.

It's why Southern Senators walked out of the US Senate Jan 21, 1861, as their attempt to block Kansas entering the Union Failed. Leading to a wave of secessionist states leaving the Union and ultimately to the formation of the Confederacy, February 4, 1861, in Montgomery, Alabama.

Wyandotte Constitution
As 11 slave states seceded from the Union, their senators left their seats and on January 21, 1861, the Senate passed the Kansas bill. The admission of Kansas as a free state became effective January 29, 1861.

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South Carolina in the American Civil War
On February 4, 1861, in Montgomery, Alabama, a convention consisting of delegates from South Carolina, Florida, Alabama, Mississippi, Georgia, and Louisiana met to form a new constitution and government modeled on that of the United States.[18] On February 8, 1861, South Carolina officially joined the Confederacy. According to one South Carolinian newspaper editor: .
The South is now in the formation of a Slave Republic... — L.W. Spratt, The Philosophy of Secession: A Southern View, (February 13, 1861).

The South had lost the ability to grow the institution of slavery, lost the ability to keep pace with free states in the US Senate, and thus had politically lost the ability to ensure the legality of the institution.

For Lincoln preserving the Union was the central theme of the civil war and the end of slavery would be one of the products of that pursuit. To Lincoln's mind it might take decades but it would happen, and he was willing to allow it to take decades if it meant averting War. To this end Lincoln telegraphed to the insurrectionist south and their would be allies, he would not abolish slavery.

July 10, 1858: Abraham Lincoln, Speech at Chicago, Illinois
I have always hated slavery, I think as much as any Abolitionist. I have been an Old Line Whig. I have always hated it, but I have always been quiet about it until this new era of the introduction of the Nebraska Bill began. I always believed that everybody was against it, and that it was in course of ultimate extinction. . I have said a hundred times, and I have now no inclination to take it back, that I believe there is no right, and ought to be no inclination in the people of the free States to enter into the slave States, and interfere with the question of slavery at all.

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In August 1862, Lincoln in a letter to newspaper publisher Horace Greeley
"If I could save the union without freeing any slaves I would do it; and if I could save it by freeing all the slaves I would do it; and if I could save it by freeing some and leaving others alone I would also do that."

This was an active campaign to entice the south back into the Union along the Status Quo. To your question early in the war Lincoln took steps to preserve slavery early on in the American Civil War. The most famous event was the Emancipation of John C. Fremont. Fremont had been the First Republican nominee for President and had lost the election in 1856. Fremont was also one of the most famous political abolitionists. During the Civil War he was a Major General for the Union.

Fremont Emancipation

on August 30, 1861 in St. Louis, Missouri during the early months of the American Civil War. The proclamation placed the state of Missouri under martial law and decreed that all property of those bearing arms in rebellion would be confiscated, including slaves, and that confiscated slaves would subsequently be declared free.

Lincoln who read about General Fremont's Emancipation policy ordered him to rescind it and stop confiscating and freeing slaves.

Lincoln wrote Frémont the next day, directly ordering him to modify the emancipation clause to conform with existing federal law—that only slaves themselves acting in armed rebellion could be confiscated and freed.

Lincoln ultimately removed Fremont from his command.

When it became clear that the civil war could not be averted, Lincoln began to make the War about Slavery in the North. Lincoln did not want to fight the war, but once it became clear the war was going to happen, Lincoln decided to make it about ending slavery.

• April 12–13, 1861 Civil War begins Battle of Fort Sumter.
• July 1862 **Preliminary proclamation** but is convinced because the war is going so poorly for the Union to wait until a Union Victory to announce it for fear it would make the Union look weak and desperate to would be European Confederate allies.
• Aug 30, 1861 Lincoln orders Fremont to rescind his Emancipation.
• Sept 17, 1862, Battle of Antietam ends technically in a draw. The Union had had the South's battle plans prior to the battle but still could not exploit the intelligence. Union General George McClellan is relieved of his command after the Battle. Non the less Lincoln declares a great Union victory.
• Sept 22, 1862, Lincoln following the "Union victory" at Antietam, issues the Presidential order #95, Or Emancipation Proclamation.

Which from then on makes the Civil War about Slavery in the North.

Question #2:
Can someone recommend sources that describe these attempts, by the Union, to temporarily re-enslave the freed people on the very same plantations? How widespread was this and how did the North's military elites rationalize it?

Detailed Answer #2
Specifically about General Nathaniel P. Banks actions in Louisiana, which another answer covered. This was more about General Banks than Lincoln. Banks was a former Republican governor of Massachusetts and long time supporter of abolitionist causes at least politically. He was charged by Lincoln to raise a force of men and re-enforce the occupation of southern Louisiana. Unfortunately Banks enforced the letter of the Emancipation proclamation and not the spirit. The Emancipation Proclamation did not free slaves in non secessionist states because Lincoln did not want to stoke revolutionary flames in the tenuous border states which the Union depended upon. If Maryland for example had left the union the Capital of the Union would have been surrounded. Louisiana already secessionist and under union occupation did not fit this criteria, and Banks policy of repatriating slaves in 1863 prompted a note from President Lincoln.

My dear General Banks,
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Governor Boutwell read me to-day that part of your letter to him, which relates to Louisiana affairs. While I very well know what I would be glad for Louisiana to do, it is quite a different thing for me to assume direction of the matter. I would be glad for her to make a new Constitution recognizing the emancipation proclamation, and adopting emancipation in those parts of the state to which the proclamation does not apply.2 And while she is at it, I think it would not be objectionable for her to adopt some practical system by which the two races could gradually live themselves out of their old relation to each other, and both come out better prepared for the new. Education for young blacks should be included in the plan. After all, the power, or element, of “contract” may be sufficient for this probationary period; and, by its simplicity, and flexibility, may be the better.
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As an anti-slavery man I have a motive to desire emancipation, which pro-slavery men do not have; but even they have strong enough reason to thus place themselves again under the shield of the Union; and to thus perpetually hedge against the recurrence of the scenes through which we are now passing.
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Gov. Shepley has informed me that Mr. Durant is now taking a registry, with a view to the election of a Constitutional convention in Louisiana. This, to me, appears proper. If such convention were to ask my views, I could present little else than what I now say to you. I think the thing should be pushed forward, so that if possible, its mature work may reach here by the meeting of Congress.
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For my own part I think I shall not, in any event, retract the emancipation proclamation; nor, as executive, ever return to slavery any person who is free by the terms of that proclamation, or by any of the acts of Congress.
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If Louisiana shall send members to Congress, their admission to seats will depend, as you know, upon the respective Houses, and not upon the President.
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If these views can be of any advantage in giving shape, and impetus, to action there, I shall be glad for you to use them prudently for that object. Of course you will confer with intelligent and trusty citizens of the State, among whom I would suggest Messrs. Flanders, Hahn, and Durant; and to each of whom I now think I may send copies of this letter. Still, it is perhaps better to not make the letter generally public. Yours very truly.
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A. Lincoln

This is referring to the area around New Orleans, ca. 1863-5. The Emancipation Proclamation didn't apply to lower Louisiana, which was already under Union occupation. It only applied to areas that were in a state of insurrection on January 1, 1863. Slaves in lower Louisiana remained enslaved until the passage of the 13th amendment on December 6, 1865.

So these people were not being re-enslaved. Legally, they had never yet been emancipated.

For a Union commander in Butler's position, there was an acute contradiction between (a) fighting a war whose avowed purpose had become emancipation and (b) being expected to help protect "property rights" over slaves. Helpful discussion in comments points out that they found creative ways of working around this contradiction, including labeling slaves as contraband.