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I think that the Kobo will not process a file if it already exists in its db, and - in older versions, at least - it does not clean the db if you simply delete the epub file. So the easiest way to make sure the new file is processed is to change the file name. There are sqlite tools available for accessing the db, but the Kobo plugin for Calibre may do all the db work for you (I'm not sure).
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