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The cover image in both MOBI and EPUB resides in the core portion of the file. It is not "metadata", and therefore can't be changed without rebuilding the file.
To change the cover in a MOBI you must convert it, generating a completely new file. With calibre you can do a MOBI to MOBI conversion to accomplish this.
EPUB files are actually just specially organized ZIP archives. You can change the cover image by converting in calibre (either MOBI > EPUB or EPUB > EPUB). You can also change the image by opening the archive (using calibre's Tweak EPUB function or by changing its extension to ZIP and viewing the contents).
If you do the latter, you need to replace the existing cover image(s) with new images of matching size(s) in the archive. Do not extract the archive components and then attempt to rebuild an archive. Rebuilding the archive from scratch is somewhat tricky.
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