Delayed Missed Base Appeal

 
With one out and the bases loaded, the batter (B1) doubles to centerfield. The runners at third and second base score easily, but the runner that started at first base is thrown out at 3rd base for the second out of the inning. The defensive coach calls time to talk to his pitcher and then decides to change pitchers and make other defensive changes. Meanwhile, the offensive coach sends in a pinch runner for B1 at second base.
 
Just as play is about to resume, the defensive coach appeals that the batter who doubled missed first base on his 2-run-scoring double. B1 did miss first base on way to 2nd base, so B1 (who is in the dugout, since there is a pinch runner on 2nd base), is called out for the 3rd out of the inning. Do all those RBIs recorded by B1 (10 minutes ago) count?
 
Call
Appeals made on missed bases must be made by the defense before the next pitch or play (NF 8-2-5 PEN). When the last out of an inning is made by the batter-runner being called out before he touches first base, any runs scored on the play do not count (NF 9-1-1a).

In the situation below, the base missed by B1 was properly appealed by the defense, so B1 is called out for the third out of the inning and no runs score.