Which denomination had the largest percent of members who now profess atheism?

Which denomination has the largest percent of members professing atheism?

As some of the comments infer: I really doubt there's going to be enough stats to answer this. Churches can barely keep track of their attendance numbers. How are they going to determine which non attendees have become professing atheists?

Nevertheless we can see a few remarks on Wikipedia’s article on Christian atheism:

By denomination

Protestantism

In the Netherlands, 42% of the members of the Protestant Church in the Netherlands (PKN) are nontheists. Non-belief among clergymen is not always perceived as a problem. Some follow the tradition of "Christian non-realism", most famously expounded in the United Kingdom by Don Cupitt in the 1980s, which holds that God is a symbol or metaphor and that religious language is not matched by a transcendent reality. According to an investigation of 860 pastors in seven Dutch Protestant denominations, 1 in 6 clergy are either agnostic or atheist. In one of those denominations, the Remonstrant Brotherhood, the number of doubters was 42 percent. A minister of the PKN, Klaas Hendrikse has described God as "a word for experience, or human experience" and said that Jesus may have never existed. Hendrikse gained attention with his book published in November 2007 in which he said that it was not necessary to believe in God's existence in order to believe in God. The Dutch title of the book translates as Believing in a God Who Does Not Exist: Manifesto of An Atheist Pastor. Hendrikse writes in the book that "God is for me not a being but a word for what can happen between people. Someone says to you, for example, 'I will not abandon you', and then makes those words come true. It would be perfectly alright to call that [relationship] God". A General Synod found Hendrikse's views were widely shared among both clergy and church members. The February 3, 2010 decision to allow Hendrikse to continue working as a pastor followed the advice of a regional supervisory panel that the statements by Hendrikse "are not of sufficient weight to damage the foundations of the Church. The ideas of Hendrikse are theologically not new, and are in keeping with the liberal tradition that is an integral part of our church", the special panel concluded.

A Harris Interactive survey from 2003 found that 90% of self-identified Protestants in the United States believe in God and about 4% of American Protestants believe there is no God. In 2017, the WIN-Gallup International Association (WIN/GIA) poll found that Sweden, a majority Christian country, had second highest percentage (76%) of those who claim themselves atheist or irreligious, after China.

Catholicism

Catholic atheism is a belief in which the culture, traditions, rituals and norms of Catholicism are accepted, but the existence of God is rejected. It is illustrated in Miguel de Unamuno's novel San Manuel Bueno, Mártir (1930). According to research in 2007, only 27% of Catholics in the Netherlands considered themselves theist while 55% were ietsist or agnostic deist and 17% were agnostic or atheist. Many Dutch people still affiliate with the term "Catholic" and use it within certain traditions as a basis of their cultural identity, rather than as a religious identity. The vast majority of the Catholic population in the Netherlands is now largely irreligious in practice. However, a 2010 study failed to locate any atheist Catholic priests.

Secularism, agnosticism, and atheism are often seen as direct (by)products of the Western European Enlightenment; as such, the Western world (not necessarily Europe), and (formerly) communist countries (whose doctrine spanned, through Russia, until China) are the most exposed areas.

If one is strictly asking about people who are baptized (presumably as infants) and then go on to be atheists, it's almost certainly going to fall to one of the denominations where baptism of infants is considered a cultural norm, even for non-believing parents. That would point us to the big national churches: Catholics, Anglicans, Lutherans. But nobody keeps track of the beliefs of people who are baptized as infants and later don't profess a belief.

More information may be gleaned from the following article on 10 facts about atheists

3 Atheists make up a larger share of the population in many European countries than they do in the U.S. In Western Europe, where Pew Research Center surveyed 15 countries in 2017, nearly one-in-five Belgians (19%) identify as atheists, as do 16% in Denmark, 15% in France and 14% in the Netherlands and Sweden. But the European country with perhaps the biggest share of atheists is the Czech Republic, where a quarter of adults identify that way. In neighboring Slovakia, 15% identify as atheists, although in the rest of Central and Eastern Europe, atheists have a smaller presence, despite the historical influence of the officially atheist Soviet Union. Like Americans, Europeans in many countries are more likely to say they do not believe in God than they are to identify as atheists, including two-thirds of Czechs and at least half of Swedish (60%), Belgian (54%) and Dutch adults (53%) who say they do not believe in God. In other regions surveyed by the Center, including Latin America and sub-Saharan Africa, atheists generally are much rarer.

4 In the U.S., atheists are mostly men and are relatively young, according to the 2014 Religious Landscape Study. About seven-in-ten U.S. atheists are men (68%). The median age for atheists is 34, compared with 46 for all U.S. adults. Atheists also are more likely to be white (78% vs. 66% of the general public) and highly educated: About four-in-ten atheists (43%) have a college degree, compared with 27% of the general public. Self-identified atheists also tend to be aligned with the Democratic Party and with political liberalism.