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Naloomi Disable online backup synching, copy what you have to local storage - eg. elsewhere on your disk, another computer, server, usb stick etc
What online backup service are you using ?
If its Google Drive then it might have done the 'tampering', see
WARNING - Google Drive Incompatible with Calibre!
Otherwise, use
Library Maintenance->Restore database - it will build a fresh metadata.db from the metadata.opf files in the book folders
Then run
Library Maintenance->Check Library and resolve any anomalies in the second phase, hopefully there wont be any
When you're happy with the rebuild you could restart the online synch - although if it were me I'd trash what I had on the online service and start over.
Once you satisfied that all is OK, including your online backup & restore processes you can trash the local backup.
BR