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The problem isn't calibre or the cloud software. The problem is you.
Calibre is single user software and the calibre library is not designed to be used on any type of networked file system.
Before you start calibre, turn off any other programs that may access the calibre library. That especially includes cloud software. But only turn off the cloud software when it has fully synced the calibre library with the cloud. If you follow these rules everything should work fine. This means that you can only use calibre on one computer at a time, if they both have the same calibre library, connected to the cloud.
If the cloud software is running and is in the process of updating the calibre library, you may loose books and information in the calibre library. Calibre keeps track of the books by recording information about them in metadata.db. But any changes you make to the files from calibre may be reversed by the cloud software. That means that calibre loose track of the books. Even metadata.db may be replaced.
I suggest that you turn of file sync with the cloud and run the library maintenance functions to try to fix any problems. Or restore a backup if you have a recent one.
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