Try logging out of your Kobo account on the ereader from Settings, Accounts, and you'll see "sign out" at the right. Then sign back in again. Make sure you have access to your Kobo password before you do that.
Are you certain the books are shortcuts only? If they're .kepub books, I think Kobo usually shows those without any extension when on the reader itself. I rarely use .kepubs other than to try them awhile ago, I prefer .epubs.
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