So, Something went wrong, I don't know what went wrong, but something certainly went really, really wrong.
I used the tool and followed the instructions, but basically... everything has been doubled. I added screenshots below. Even the music is playing twice simultaniously. As you can see I have a copy of a smoothed texture and one without running twice over.
I think I discovered why, while poking through, I noticed it added the smoothed files beside the unsmoothed:
So I know the 'why' but not the 'how' nor how I can... fix this?
This is strangely hilarious, though.
EDIT: So I figured it out, I said 'yes' to seeing the before and after of the smoothing program and it seems to have been the cause of this issue. Still keeping this and the screenshots for further possible investigations.