If book files that you added to the documents folder are disappearing after a while (or sometimes it takes a reboot to manifest), then I suspect you have a corrupted flash chip.
https://www.mobileread.com/forums/sho...49#post2810749
Not much you can do about hardware damage, I'm afraid.
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It is seriously not normal for files to disappear on their own. That these are, implies the chip is unable to actually write the changes to disk.
Generally, it appears at first to still be there, because the file is cached in memory. Rebooting is a good way to
force the memory cache to clear itself, revealing the true state of the underlying storage.