[Adoby]

Calibre doesn't delete random books. It has to be some other reason that you haven't mentioned yet. We can only speculate. For instance backup or cloud sync software that is active and working while calibre is running?

Or partial backup restore into an existing calibre library structure, instead of first deleting the whole library and then restoring all of it from backup. Or restoring to a new place. Since the database expect books in certain folders, restoring folders without restoring the database, or the database without the folders, will cause havoc. Seemingly random havoc since some folders may be OK but others are not.