Check your Virus Vault and Log .
I suggest that you exclude the Calibre Librry folder (and All Subs), Further, I heartily recommend you make your Anti Virus
ASK what to do when it discovers
file x is a bad guy. I have not seen a lot of False Positives, but some would have destroyed any database usability .
Another Database
sync killer is
disk cache. Some pieces get written (Metadata in this case) and other pieces were in cache, waiting to be written to disk, when something went sour

Again, disable write behind caching. It exists to make you think you are done sooner than you are and give back control of your program (while it plays,'catch-up') .