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I think the problem is that Calibre and Kobo use different protocols for file-names of multiple-author works. So when Calibre transfers a single-author book, Kobo just takes the file as-is, but for a multiple author book it changes the file name. Then, when Calibre is reading the Kobo it sees a different file-name and assumes there are two different books, one on the computer and one on the Kobo.
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