retouching a base

[bananasareripe]

here's the situation:
the bases are loaded with 2 outs. On the first pitch the batter hits a foul ball out of play. the runner on third stands a foot off of the base without touching it. The pitcher steps on the rubber and makes another pitch which was a ball. the pitcher then appeals to third about whether the runner re touched the base after the foul ball, and while he does this the runner is standing on third. the umpire calls the runner on third out and its the end of the inning.

im pretty sure the appeal was too late, and is there even a rule regarding retouching the base?