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I have both kepub and epub selected for my KLC, and the epubs are converted automatically when they are sent, without leaving another format in the Calibre library.
Calibre will choose an available format from what is preferred, and will only create a local conversion if none are available. If epub is available, it will be used. The conversion to kepub is handled in the device driver, based on the "Use KOBO viewer..." setting.
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