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It's not possible to convert PDF to PDF in Calibre without losing quality because it gets converted to XHTML as an interim stage and Calibre has to do a best guess of how to reconstruct paragraphs (if you've ever tried to do this manually you'll understand the difficulty).
If all you want to do is change the cover then a proper PDF editor would be an easier option and would retain all the formatting. Acrobat Pro is one option but, of course, it's not cheap.
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