As far as I remember, saves, replays, settings, and some other information are stored in my documents.
It's always a good idea to back them up.

P.S. Check the scenario in a clean game – without adding all your files (you'll need to add the saves, of course).
It's best to replay the scenario.
Also, try replaying the scenario with codes.
To clarify, quickly use codes to complete all the tasks, get to the desired location, and see if the script works.
If it works, start over legally.