Sorry, I don't know what you are doing. The only "kepub" directory on the device is ".kobo/kepub". This contains any books purchased from Kobo and downloaded to the device (either over WiFi or using the desktop application). If you don't have any files in there, then you haven't downloaded any books. But, maybe the problem is that the files in there do not have an extension. This is expected. But, you shouldn't be looking in the directory. Calibre does not use this when communicating with the device.
It might be better to tell us what you are actually trying to do. If you start calibre and connect the device, calibre will display the list of books on the device in the device list. And it will mark all books on the device that are in the calibre library with a green tick. What else are you trying to do?
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