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Don't try to use the kePub version downloaded by the Kobo desktop. If you go to "My Library" on the Kobo site you should see a teal/blue button in the books listing to download either an ePub with Adobe DRM, a DRM-free ePub or a DRM'd PDF (rare) depending on what's available.
Once you have the file downloaded you can add that to Calibre.
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