EPUB doesn't have an official way to specify a cover. instead most EPUB producing programs just put the cover into the "first page" of the book. calibre does this as well, however, it also marks the first page as being the cover. Using that marking it is possible to "replace" the cover, however if you get the epub file from elsewhere and it doesn't have that marking, it's not possible to know if the first page is the cover or not.
In fact, I don't actually recall if the current code tries to set EPUB covers or not.
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