You can do that, and it should work, theoretically. But I'd suggeswt after you've partitioned the drievs and applied a new windows install, to reinstall yur SH3. This way it will be in the registry too. Otherwise it won't, but it should\nt make a difference and you should be able to play on the copy as well. Only thing you probably won't be able to do is launch the game thru a start menu shortcut (I think), because IIRC those use registry values.
Anyway long story short:
- A copied SH3 folder and all associated folders onto a new partition should work. Launch it through the .exe file in the copied folder.
- Best to reinstall SH3 and place your career/s in your documents (from backups you made)
- Backup everything before doing anything. (Just to remind, as I forget to backup before I do something often)