I have already heard of daul-retailing, then going on Live, but since the files are still there, M$ can still pick it up.
MS does not scan your harddisk for files - at this time - it will just scan for size, and different keys/eeproms. I personally have used live with dual retail for a while... if your modded, NKPatcher will block live access, so only when booting retail BIOs will you be allowed to connect to live. So, theoretically, you are safe to use live in dual retail mode, as long as you are not modding etc.
This works.
Another option, instaed of uninstalling your softmod, is turning it off. This basically a longer winded way of using dual retail mode...
It's up to you though...