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It is HIGHLY discouraged, to use any other method to Delete or clean a Calibre Library.
If you are ending up with unintended 'empty books' (Some of us create those to document our Paper Library), then your process is incorrect.
Calibre cleans up old News (if configured),
All other corruption is caused by OTHER programs interfering with file/folder operations. Most common culprits: CLOUD sync of the Library while Calibre is running. Over active, A/V scans is a close second
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