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the good news is that you should not have lost any books because dropbox keeps all "deletions" for 30 days & allows restores.
personally I'd do this:
1. create a new calibre library - on a local drive, not in drop box.
2. then add books to it from dropbox until you have recovered all books and rebuilt your metadata ( using calibre add books function)
3 once you are sure that you have a 100% good local library, then delete all th dropbox stuff via one pc.
4 once that is done, allow the other pc to also access dropbox - it shoudl delete all of it's records also when it syncs. If not then assist it manually
5 going forward use dropbox only to hold a backup copy of your local library
others have written a lot about steps 5, using a sync utility like free file sync , set to one way mirror, & use a script to run it every time you close calibre & you are into automated processes. I have my backup in dropbox & I have 2 PCs able to access that dropbox account - it has never screwed up. the 2nd PC syncs as it should to dropbox whenever I turn it on- I see "recent changes downloading" so I know that sync is happening OK
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