First, you must start the game, be sure that steam cloud is on. Go to Load Game and delete all saves, then go to the C:\Users\*username*\Saved Games\Arkane Studios\Prey\SaveGames and delete all in the folder, then start new game, save and just quit, when you get to the moment where progress is superimposed, it's all will be gone, and be just like in ur first walkthrough.