Definitely don't go hacking around with the covers in calibre's library by deleting them...
if you do a search for cover:false it will show you which books do not have a cover image associated (and vice versa). And the bulk edit dialog has options on there to both remove covers and extract covers from the ebook (bearing in mind that the latter will overwrite any cover you might have downloaded). Any time you download a cover or extract a cover (there is a button for that on the single edit metadata dialog too) that is the source for the image. or of course you can generate one using calibre, or using this plugin.
Last edited by kiwidude; 07-17-2012 at 08:44 AM.