I'd suggest just waiting a bit. I've never had that sort of trouble with Kobo, but that's the exact same kind of trouble that caused me to stop buying from B&N: downloads not being immediately available (page errors... download button not available ... blah, blah, blah). Sometimes I had to wait almost 24 hours before I could download a stand-alone file from them (even though it was immediately available if I wanted to access it through the Nook app).
Hopefully it turns out OK for you.
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