Batter Missing First Base

[tibear]

Question on another umpire site that I want to clarify.

Situation: Runner on 3rd, 2 outs. Batter hits a clean double to score the R3. However, defence successfully appeals that batter never touched first base. Does R3 score? The other site claimed that 4.09 (a) Exception 1 states that the run shouldn't count because the out was called "before the batter touched first base."

I always understood that appeals did not affect prior runs, ie appeals were not force plays but timing plays. Thus all prior runs on appeals were valid.

I'm sure someone will set me straight.