Apple IBooks periodically wipes my library without warning
This is a known issue, with multiple now closed discussions of this “feature” going back to at least 2017.
In short, if your iPad reaches some pre-set storage percentage, Apple removes all your book files from IBooks storage without warning.
Clearly Apple sees some business advantage in this: one more way to push people onto iCloud do everyone has to pay them monthly forever.
I mostly came here to say you others: you have to back up every pdf or book to your Files separately from IBooks and then onto another device not controlled by Apple, or you will lose work & files. They are big retrievable once removed. Apple may try to back them up to iCloud if you have not turned that off (you should).
Finally, to Apple, this is how you lose customers. It’s nasty, awful behavior and I hope it eventually rebounds on you.
iPad, iPadOS 16