Can you supply the name of the book? The only kepubs I've downloaded from Kobo that do not have a download option in the Actions menu are ones that were part of the Kobo Plus program.
As for copying a file from the Kobo desktop app to calibre? The Obok plugin will do that but, in my limited testing, it will show Kobo Plus books as not being DRMed and so the import will import an encrypted copy.
I tend to regard Kobo Plus books as I do library and Kindle Unlimited books. They aren't mine and I do not even bother trying to remove DRM to keep them around so basically, this is as far as I am willing to go with offering help.
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