I can't help you with the cover art issues (I don't have a Nook, and barely touch Calibre), but for epub to epub: the conversion will remove weird settings in the original (like wide margins good for viewing on a computer screen, or a too-small or too-large base font size) and allow the reader to use their own settings. It can also remove bad CSS elements or bad HTML sections, if any. Allows for a TOC to be made, and so on.
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