Appealing a Missed Base?

 
With two outs and a runner on 3rd base (R3), the batter (B1) doubles. R3 scores and B1 ends up on 2nd base -- but B1 missed touching 1st base on his way to 2nd base.

The defensive coach goes to the mound and replaces his pitcher. The new pitcher completes his 8 warm-up throws and then the umpire puts the ball in play. At that time, the new pitcher throws over to first base to properly appeal that B1 missed first base. The base umpire calls B1 out for the 3rd out.

The coach of the offense objects for several reasons:
- the defense waited too long to make the appeal
- the defense replaced the pitcher
- the new pitcher threw to an unoccupied base, so he balked.

The defensive coach now even wants R3's run taken off the board.

What do the umpires do?

Call
Since there was not a pitch or a play, the defense still had the opportunity to appeal B1's failure to touch 1st base. While the defense could have appealed while the ball was dead, the live ball appeal was also valid. B1 is declared out for the 3rd out of the inning.

Since the batter-runner never touched 1st base and was declared the 3rd out, R3's run does not count (NF 9-1-1a).