What I do is much less elegant than theducks solution, but it is pretty easy. Many ways to skin this cat. My workflow:
First I add the new cover I want in the metadata editor, but do not "polish" the book to get it into the book file. Then:
1. (optional) Open the book in the editor. Right click on the existing cover file - the one you want to keep - and export it. (I have a "covers" directory specifically for handling covers, to avoid confusion with other images. I rename it to keep things easy. While it is exported, I also edit it, if I need to, with an external program like GIMP.) [This export is optional, but since I so often edit the image I just always do it. So many old cover shots are badly faded, and I brighten them up.]
2. Still in the editor, I add a brand new html file (menu: file/new file) - which I name altcover.html - , import the exported cover file (menu: file/import files into book), and place code for it in the new html file. I have the code in my master "cheater text file", so I just copy it in and then point to the image file name I want. [If you didn't actually export, just point to the existing cover image]
3. Then I exit the editor, and go ahead and polish the book, with "update the cover in the book files" checked.
Now I have the original cover in a separate file, which is where I want it for TOC reasons, and the nice new cover where Calibre puts it with all the nice correct and complicated coding.
This sounds way more complicated than it is, when I write it out. It actually only takes maybe 20 seconds to actually do it. Of course you can put in more than one alt-cover image this way--as I often do for old pulp SF and mysteries!
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