Yes, and calibre's send to device can update BOTH of those locations, but only in supported formats: AZW3 and EPUB.
As far as calibre is concerned, covers ARE metadata, although not a type every format supports: i.e. MOBI.
Go to your book in calibre, right-click and select polish ebook, make sure update cover is checked, and click ok.
Then view the book in calibre viewer -- you should see the new cover updated.
The old version will be saved as ORIGINAL_AZW3 and can be right-clicked to "restore the ORIGINAL_AZW3 format", so it's perfectly safe.
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