One feature of Calibre that I really like is the ability to normalize various format settings (paragraph breaks, etc) and to smarten quotes during the conversion process. Because I have a Nook, and most of my books are ePubs from Gutenberg, I have to convert ePub to ePub manually in order to get this behavior. Is it possible to have Calibre always convert to ePub (even when the source is ePub) when transferring to my Nook, so I automatically get these enhancements?

What I am really aiming for is a way to keep source files unchanged. This is because conversion is an inherently lossy process. My rationale is that if Calibre gains an enhancement in the conversion process (e.g. smartypants becomes even smarter and produces the proper quotation mark even more often), I want to be able to convert from the original again. I can currently keep backups easily enough, but if Calibre can do on-the-fly conversion without touching the source, I would be ecstatic. I never read on my computer so it doesn't bother me if they have straight quotes, bad paragraph breaks, etc. I would just like an unchanging source for any future conversions.