Wipe it out, probably. If you can copy the userdata folder or even the entire TS12 folder to a different location on the same drive, try selecting the Trainz.exe file in that folder and run it from there instead of the shortcut. Or do a new install then copy the userdata folder from the backup and paste that in, whatever the last files copied in are will overwrite previous files if you answer yes to overwrites, so it's simply a matter of copying in whatever files you want as the last set.
I'm curious how you know the registry is corrupted, what are the symptoms? Usually if there's something bad in the registry it's not just one game affected, and I've had no problem running copies of Trainz on another computer without actually installing, so it really doesn't need any registry keys at all to run. Might be just the shortcut itself that's bad, you can create a new one by copying trainz.exe, change to the desktop and right click, select "paste shortcut".
Other item, if the registry itself actually IS corrupt, have you tried a system restore?