I've come up with a kludge of my own to work around the limitation: Whenever I create an optimized version of an eBook for my Nook, I add the original with a suffix of "-orig" (i.e., "foo.pdf" would become "foo.pdf-orig"). This way, I can keep both the original and a modified PDF in Calibre. No silver bullet, though, as you'll again face issues if you create multiple optimized versions, say, for multiple devices.
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