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If you use the KoboTouchExtended device interface plugin you can have it auto convert ePub to kePub on the fly when transferring to the device. I can't remember if it does this by default or if you have to check kePub when you customize the plugin.
The kepub output plugin lets you do a conversion to kePub within Calibre as opposed to on the fly during transfer. There may be a way to set it up for on the fly conversion, I'm not sure as I've never used it.
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