I have books appear to go missing after an upgrade.
On the one occasion I was able to check the books were missing before the upgrade but didn't show in the book count. (I had just backed up database to another computer which still had prior version of calibre installed) and/or had no formats (formats:false)
AFAIK the books went missing due to conversion errors or remove book errors which were caused by my having the book open in a viewer when the operations were being performed.
Converting epub to epub will give an error message if book is open in non calibre viewer and deletes the epub format. Metadata is still there but no epub format. If epub format is only format than book must be reimported
Removing book will give an error message if book is open in non calibre viewer and deletes the book from GUI but leaves it in folders directory and doesn't decrement book count. AFAIR when new verion is installed it seems to get book count correct again.
I opened a ticket on this a while back
https://www.mobileread.com/forums/sho...ghlight=ticket
Hope I have not been too confusing.
Helen