Sometimes, mundane explanations are best.
I had been imagining all sorts of convoluted explanations as to why exactly the books with Tetrimonic records were missing. Perhaps they were purged, along with other works declared heretical after the Moral Reforms. Or perhaps they have been moved to a safe place, a "monk hole" for books, exactly to avoid the purge?
In the end, it was the restoration crew of the library itself who moved the books, just recently. No-one had touched them, before that. They were moved not out of any concern about their potential heretical nature, but simply because the bookcase needed to be repaired. They had been stacked somewhere else, on the floor in a niche at the side of the library. And that is also why the bookcase had 'disappeared'.
I found the book that I was looking for, the "Vita Magistrorum Magnorum - Tetrimon IV", a contemporary biography of grand master Tetrimon IV, written by his followers. He opposed the Moral Reforms and is said to have hidden artifacts from the Council of Apostles, to prevent Emperor Heideran V from finding them. There was also a rare copy of a volume of the "Deliberationes Concilii Apostolorum", records of the meetings of the Council of Apostles, from the time of the Moral Reforms - an important historical document. It is part of a very long series of recorded debates, going back millennia, that were considered part of Scripture before the reforms.
Undoubtedly, now both books are deeply heretical, and they would have been purged right after the end of the Moral Reform wars by the Theology Council, which was then newly created by Heideran V to replace the Council of Apostles. There may still exist copies in the Tetrimon Monastery, but if they have copies, they do not let anyone near them. Luckily, Baron Redwolfe's abandoned monastery remained untouched and today falls outside of conventional Tetrimon control.
These books are not for the general public, as it could harm those untrained to withstand heresy. But for the trained theological expert, armored by a strong faith, it ought to be possible to study them for the benefit and glory of the Empire.
