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So I guess everything is fine now and I hope it remains so. I just wish I knew what caused the problems in the first place.
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Perhaps you had a an ebook or file open in a non calibre app?
Perhaps it was the infamous gremlins.
Another quick check to perform is type
formats:false in the searchbar to see if you have any books with no actual book files.
Glad all is well
Helen
BTW it is possible to have errors even doing things the approved way. Forgetting to close a book or file open in a non calibre app will result in that book not being deleted.