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It sounds like you have the "KoboTouchExtended" plugin installed and enabled. That will only send kepubs to your reader, that's the main purpose of the plugin.
To get epubs again, you'll have to disable that plugin, and then enable the standard "KoboTouch" plugin that's included with Calibre.
I have 1.16.0 installed and just tried transferring books and they're still epubs using the standard KoboTouch plugin that's installed.
Edit: I should add I'm using 2.4.0 firmware, but I don't think the newest reader firmware changes how the plugin behaves when sending books to the reader.
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