Generating a cover only simply replaces the cover file stored within calibre's file system, it doesn't touch the ebook itself. When you send a book to a device like an ePub, calibre will attempt to replace the internal cover with that latest cover image. However in some circumstances the epub does not internally identify which is the existing cover that is in there, so calibre can't do that replacement. Hence you see a different cover in the epub on the device versus that you see in the calibre library.
So you need to do an epub -> epub conversion in calibre before you send to the device, during which calibre will "force" the cover into the epub. From that point on the cover is identifiable by calibre so it is able to further replace it in future if required.
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