You should probably be asking bout this in one of the E-Book Formats forums. That is the place on MobileRead where e-book creation and publishing is discussed. (A moderator can move this thread if you ask.)
My understanding is that when you publish on Amazon using KDP you also upload your cover as a separate file and that replaces the cover in your book. So how your cover looks now in the EPUB isn't going to be important for that use case. (I still recommend that you fix it anyway.)
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