[eschwartz]

That only happens when the original cover was not properly marked as a cover image. For example, the MOBI format simply doesn't support cover metadata at all (the Kindle will simply assume the first image in the book is the cover image).

calibre has always tried to determine the existing cover and replace it. The situations where it fails, and keeps both, is regarded as a bug (which cannot be fixed as it requires human-level intelligence to make that judgment call).

...

If you want to keep both cover images, your best bet is to use the Edit Book feature and add one cover as a cover image and the other as the first "page" in the book.