Protest upheld, now what?

[jimfreeman]

Situation: PU Only, 11/12 y/o game played under modified OBR. Top of the 6th, 2 outs, home team up 2-1, R1, R2 & R3. BR hits grounder to F3 who deflects it and it hits R1. PU rules runner out for being hit by batted ball, 3 outs, game over. Offensive manager is protesting for misapplication of 7.09(m). I've been led to believe that the umpire saw the ball hit F3. If that is true and I uphold the protest, in the restart would the situation be:

R1, R2 & R3
2 Outs
Score tied 2-2

Also, besides "Did you see the ball hit F3?" and "Did R1 INTENTIONALY deflect the ball?", any suggestion as to any questions I should ask the umpire? Should I interrogate the offensive & defensive managers?