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@GoldThreader -- fortunately Calibre can be self-healing.
Calibre, Library Maintenance, Check Library (Step1.jpg)
This is a 2 step process
1. If it finds no errors, tell it you want to check if the files match the information in the data base
2. Things like manually deleted files ("missing book formats") are fixable (Step2.jpg) and Calibre will delete them from it's database
BUT all of the hands-off advice above should be followed, since I'm SURE it's possible for a creative user to do SOMETHING that cannot be fixed
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