This kind of damage is almost always caused by something/someone messing beneath the Library skirts:
Rogue A/V. Tame it
exclude the Library folder if needed (the books were checked in the originating folder before they were added)
Cloud/backup file locking Always pause while Calibre is running
And the most common...User renaming or replacing with anothe file that has a sligt case difference
exceptions: power or drive failures, but those usually lose the (write cached) book file