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I had the same problem, its really easy to resolve. Basically you have to keep in mind that calibre use the kobo database to know what books are on your device. That database need to be updated but it can only do so in the original kobo environment.
Therefore if you import books while being in koreader that database won't be updated, a quick solution is simply to connect your device in USB while in the kobo environment and just disconnect (safely!), the db will automatically be updated and your books should show up in calibre.
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