What OS are you using? Win 7, 8, 8.1 or 10?
You shouldn't have any problems reinstalling SH3 as long as you do not put it in Program Files or Program Files(x86) folder. Follow this advice by BL!TZKR!EG....
http://www.subsim.com/radioroom/showthread.php?t=220927
SH3 Commander should be ok..... but you never know.
Note... some have installed SH3 in the UBI folder and it works. Most tho make a folder on C Drive and call it Games , and install SH3 there.
Good luck on a good install next time around.