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Yes. Select your book in the Calibre library window and then Edit Metadata. You can drag-drop your new cover over the old one (or the big plain brown one if you don't have an old one). This won't put the cover into the PDF but it will now be your Calibre cover.
If you did a conversion the new cover would be placed inside the converted book, as page 1. But as mentioned above, converting from a PDF will always degrade it.
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