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I would disagree with that statement. Why would kepubify have a calibre option where the file extension of the output file is simply .kepub if kepubs were strictly for being copied directly to a Kobo?
When one acquaintance of mine decided he want to have kepub as his base format in his calibre library, we used a batch file and kepubify to generate the kepubs and then added/merged them into the existing calibre library. Started it running and relaxed while it updated the ~500 books in their library.
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