To extend what Charles said, calibre keeps three files for each book, the original book, which includes an internal cover image, a metadata file, and a cover image file that contains whatever you edited it to in the calibre edit metadata window.
I'm going to go out on a ledge here since I haven't looked at calibre's source code, but I think that while calibre maintains a separate copy of the book cover as an external file, if you export the book, for instance by using the Connect/share Connect to folder facility, the exported book will have the calibre cover and all of the edited metadata instead of the original.
I've been meaning to clean up my epub files by exporting them all with Connect to folder, then establishing a new calibre library and importing the exported folders. That way if I copy off a book for a family member they'll have the benefit of the work I've done in my calibre library.
If anyone thinks I'm going to shoot off a few toes by doing that, please speak up:-)
Last edited by ellett; 08-23-2012 at 06:40 PM.