Did you try long-pressing on the book and selecting "Refresh cached book information"? Sometimes I'll import a bunch of books at a time, and one or two covers don't show up, but a refresh fixes it. Also, navigating to a different folder and then coming back to the one where the glitched covers are.
Otherwise, are these ePUBs? You could try Calibre's "polish book" feature just to update the cover in the book file, then resend that to your Kindle.
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