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I never added books in another way than via Calibre.
I did however get many duplicates (for various reasons, but often because Calibre did not show me all the books!), and I removed some via Calibre and others directly in the library, but always by removing the containing folder of the book.
For unfathomable reasons, I got myself many books without any format (about 10000 out of 50000) I am dumbfounded, to say the least!
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