This message board is for the program UFT, not FTM. I would suggest that you post any further message to the FTM message boards.
If you have more than one shortcut on the desktop and they all point to the same program, you will be updating the same file no matter which one you use. If this is the case, just right click on the shortcut and select the option to delete it. You are not deleting the program, just the shortcut.