Quote:
Originally Posted by rcentros
MGlitch gave the solution. Just archive the book you don't want to sync. It's still stored at Kobo, but it's not seen when syncing. That way your side-loaded book won't be overwritten. Almost all my Kobo bought books are archived.
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It won't be an issue really as the Calibre side loaded copy and the Kobo synced copy will have two different filenames.