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So far, I keep multiple backup copies of my stuff:
a) the original DRM-ed version of the book with applicable unlocking information because sometimes the "tools" read things incorrectly due to lack of information and their accuracy later gets adjusted
b) the DRM-free version of the original, in whatever file format the tools spit out after liberation
c) a converted copy with annotations for fixing typos, major formatting errors, etc.
d) a copy of the fixed and tweaked unpacked files I work from when I make a "clean" version following my notes
e) said "clean" final version which then goes onto my Kindle for keeping
For my MultiFormat books, it's much the same. I keep a copy of the original ePub/whatever, even if it's completely messed up in its original state, for reference purposes.
One day I'll package up all the tweaked files into proper ePubs (I use ePub structure and conventions anyway, just haven't bothered doing the mimetype/manifest stuff) because Mobi is really a rather shoddy format by today's standards (except for its dictionary support, which is quite good), but for now I'm content to leave my unpacked and modified folders o'stuff as-is and only output Mobi "final" files.
Long story short (too late!): my vote is you leave them as whatever you get when the stripping tools are done, unless you need to convert to put them on a particular platform. And even then, keep copies of the originals around, just in case.
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