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Medieval scholars knew about palimpsest. They knew that it was impossible to entirely scrape a parchment clean, and they also knew that it was possible to read the underlying text, though very difficult. This was especially true in the East -- modern Greece, Turkey, Iraq and Iran.
Much of the East's store of knowledge was lost during the early Crusades, when the Pope basically diverted tens of thousands of local barbarian warlords from killing each other thrice weekly to go make war on a technologically sophisticated, highly organized, wealthy enemy thousands of miles away from the home supply lines, in a climate hostile to the Crusaders. (A cynical part of me wonders if the Crusades weren't intended to fail as a military expedition, considering they mostly did, but to succeed as a social and economic restructuring policy, which they kinda did, and as an informational transfer policy, which was the biggest success.) Most of the surviving palimpsests come from that region and that time period.
We know that the arriving Crusaders didn't stop to ask if their victims were Christian -- they merely assumed that anyone dressed for the climate had to be an infidel. The first sack of Constantinople was by Christian Crusaders, not Muslim defenders. The Northern European Christian Crusaders were appallingly ignorant, astonishingly incurious, and brutal (in general. There are always exceptions.)
It seems likely to me that well-educated, scholarly monks and scribes in areas likely to be soon sacked might intentionally hide their more controversial books -- such as Archimedes -- under piety to protect them, knowing that in time, people would figure out how to read them again. They'd already seen enormous technological improvement -- the invention of the practical mirror, the lens, and some significant improvements in medicine -- and had faith the trend would continue. (It did.)
The senior monk in charge of the scriptorium didn't get the job by being disrespectful of knowledge, and even if brought into that position by a reactionary -- and reactionaries have always existed -- there have always been an equal number of subversives. Since they knew they couldn't entirely destroy a text, I can't help but think they used that when it became the last hope.
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