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Yup, calibre users have a hard time trying to sync because, by default, calibre (at least the viewer) stores its own files within the epub container.
You can disable this on calibre settings. But there're a zillion things that could make calibre to modify the epub. In each case the result is simple: book hashes don't match and each book, as slighlty modified as it could be, is treated by the sync server as a new book.
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