The database only lists the books it successfully recovered, but all the files should remain intact. So I expect that both libraries have the same files, but their metadata.db's each list a different subset of those files.
Restore database
cannot recover non-existent files, so everything is still in the backup.
Dropbox probably created numerous "_____'s conflicted copy at %date", which messed up the database tracking.
Re-adding from one library folder should suffice, as the Adding books process does not expect a specific format for the filenames. It will add all books, whether they showed up in the database or not.