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The correct way to handle this is to:
- Check that Calibre has the correct library folder for where all your books are located.
- Use the Library Maintenance option in Calibre and select Restore database. This will then use the .opf files stored with each book to restore your database to the correct state.
- Use the library Maintenance option and select the option to check the database and library. This will highlight any files that were not handled correctly by the restore.
If you have already created duplicate entries for your books within the Calibre library folder then the process above may not work perfectly. I would also suggest that before using it you make a backup of the current library folder somewhere else on your system just in case it is needed.
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