The change when you open the room the first time, is that the main menu changes (the girls have a "white aura in the background" and in the upper right corner there is a green sphere).That is fine as I will be starting from the beginning. In the file in appdata I see all the save files plus the persistent file. I am assuming that if I delete it then the game will create a new one. I will save the original file for now just in case.
As for the ending: I am guessing that it will be based upon my choices which if I start at the beginning should produce the ending I want. I read what you said in the forums about how the ending are determined so I really want the decisions I am making in this play through to be the important one's anyway, not the one's I initially made when I didn't understand the game yet.
Thank you for the help
Edit: I deleted the entire file and started a new game. It created a new file with a new persistent data file in it as well. It looks like I am good to go.
If you see that, you still need to clear the persistent