You can try cutting the relevant folder from My Documents and pasting it to a backup location and then returning the files there to the new folder that is created when you start over to see if it works.
However if you have had two different installations of the game, one modded and one not, referencing that one folder and writing/reading files from it, IMO you would be better off to get rid of it entirely and start fresh with different folders for each installation to avoid the risk of corrupted and/or incompatible files botching things up.
That's if you can make multiple installations work with Steam + MultiSH3, which as far as I know, is not an option. To the best of my memory the Steam version of the game only allows for one installation and that's it. I'd ask for input from other Steam users on that issue before starting over with a fresh setup and then finding out that it won't work for you.
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