Note1: If you have an epub without a cover, and just add a cover in Calibre, you need to (re)convert the book so that new cover is packaged into the epub.
Note2: The Kobo caches the cover art, but doesn't seem to delete this cache when you delete the epub from the device. If this is the cause of your issue, delete the epub from the kobo, then navigate to \.kobo\images folder and delete the 3 cached image files: 'file____mnt_onboard_[PATH]_[FILENAME]_epub - [FORMAT].parsed'
You'll find 3 of these cache files per book, in 3 different [FORMAT]'s.
Once you've deleted the epub and these three files, unplug and replug the Kobo, load the book back on and the Kobo will re-extract these thumbnails when it's processing that book.
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