I started a new game again with 0.40, but with my previous saveslot still in this game, so I didn't delete anything.
Just got to choose my ultimate desire without Nameless telling me that I tried one of my tricks again.. So I guess it works if yoy start anew?
Haven't tried it out yet but maybe you can delete your current saveslot, anything that's post-ultimate descision and try again on a saveslot prior that event with Him?