You can use the Kobo Output plugin to do a conversion. This is basically a conversion to epub followed but the kepubification that the extended driver does. Once that is installed, disable the KoboTouchExtended driver. Then in the configuration of the KoboTouch driver, remove "epub" from the supported formats and make "kepub" the top format. After doing that, when you send a book to the device, it will be converted to kepub before being sent.
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