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Which KoboTouch driver are you using to send the ebook to your Kobo? If you are using the KoboTouch driver, it will send epubs. If you are using the KoboTouchExtended driver, it will send kepubs (.kepub.epub file extension).
If you have KoboUtilities installed, you can switch the active driver from it's menu. Otherwise, you can open Preferences => Plugins, search for kobot and disable the KoboTouchExtended driver and enable the KoboTouch driver. If you have done any customization in the driver, you will need to copy it over.
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