I know this is not exactly what you are asking, but.... What I do is have 2 partitions one exclusively for Windows and the other for all CarPC related stuff. Music, Videos, Frontends, etc. That way you can have the Windows partition small (about 6-10GB) and dedicate the rest to other stuff, also you don't have to worry about losing any configs if you need to reformat (assuming you redirect My Documents, etc)
As far as a postmortem move you wish to do, I am guessing that if you just reinstall MapPoint on to another partition it will be happy. Theoretically you could just move it and then update all registry references, but that's alot of work.