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I also suspect that what has happened is what @PeterT said. The first book was substituted with the second one. Calibre plugins update Kobo's internal database with the metadata of the new book, but the internal structure of the book is also on the database, and Calibre doesn't update that, so the new book has a different internal structure and Kobo can't match the internal files of the old book with the ones in the new one.
In these cases, when I have a duplicated book in my Calibre library, what I do is modify the title of the book so I can see quickly the reason to have them duplicated. For example, in my case I have two versions of the book Arabella by Georgette Heyer, one in Spanish and one in English, so my books have the title "Arabella - Espaņol" and "Arabella - English".
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