There is a program out there that can fix some of the metadata for a Mobi file. It's called Mobi2Mobi. You'll have to search the forum for it.
You can add in a new cover, with it, but you cannot remove the cover that's already there. Mobi is not designed for these sorts of changes. You'd have to unpack the Mobi to fix the cover and then repack it. There can be issues doing this. It may not always come out the same.
This is why some convert to ePub, do the work in the ePub, make sure the ePub looks OK and then go back to Mobi from there.
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