Most of the time if I only want to update the cover of an epub I drag the new cover into the metadata cover box, save it, go to that book folder in the calibrelibrary, open the epub with winrar, drag the cover.jpg (or cover.png) from the same folder into the epub so it replaces the existing file.
The only time it does not work is with epubs which do not have a cover in the first place. You cannot add a cover with this method, only replace one. It also won't give you a metadata page.
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