After you add "edit" a cover to an epub in Calibre, check just the epub file in anohter ereader, you can use the ereader that is part of B&N's pc ereader or Adobe Digital Editions "ADE", verifying the cover is embeded in the epub. If not, back in Calibre reselect the book, and convert to epub, that will embed the new cover into the actual epub file.
Personally I don't use Calibre to side load epubs, I do use calibre to do the above cover process, and then directly copy the edited epub to my Nook HD through windows explorer. I have had to add about 40 covers in last 3 or 4 weeks and the process I describe above while not one click, works 100% of the time.
Like yocalif said, after you edit the cover you want, convert from epub to epub and it should show up on your Nook.