Well, I'll try.
When you say the pitcher was "preparing to deliver a pitch," I assume you mean he was in his windup or was committed to the plate if he was pitching from the stretch.
Under OBR, the only time the ball is NOT immediately dead on a balk is if the pitcher delivers a pitch or makes a pickoff throw and throws it away. Since neither of those two things happened, the ball is dead and the balk is enforced.
Now the umpire calls off the balk. I don't think he can un-kill the ball however, since the only way it can be made live again is for the pitcher to be on the rubber and the umpire calls "play."
So I think the runner has to go back to 3rd (his Time Of Pitch base).