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One thing I have found with calibre (unless this has been changed/fixed) is that if you import an ebook into it, and you already have the ebook in another format it will add the ebook as a new book to clibre rather than just add the format to the existing book.
Not sure if adding as a format is 100% possible due to the meta data not being readable from some file types.
So, I think you will have to find out some other way to identify duplicates.
BOb
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