Scenario from Adv. Camp

[Big Slick]

R1 on 1st. IP/CO is called; batter makes contact. R1 makes it safely to third. BR misses 1st but makes it safely to 2nd. Defense appeals. BR is called out. Offensive coach comes out asking for you to enforce the penalty for the IP/CO.

Originally Posted by mbcrowder

The runner may have passed the base, but they did not advance safely to the base. Enforce the IP/CO. (Similar logic to a 2-out BR who missed first and makes it to 2nd, appealed at first negating a run - run cannot score on a play where the BR is put out before safely reaching first base)

Well, depends rule code. In ASA/NCAA, there is no enforcement of the IP/CO, as all runners and the batter-runner obtained at least a base, therefore removing the option for the offense. Therefore, the play stands (BR is out on appeal, R1 remains at third).
A similar play happened in 2011 in a NCAA DIII regional, BR hits a double on an illegal pitch, but misses first. The defense makes the appeal and the umpire (properly) rules the BR out. Unfortunately, the offensive coach (who's pitcher was having IP problems of her own, but that's a different story) argues about the IP, and the umpires (erroneously) allow the batter to bat again.

In NFHS, the offensive coach always has the option if an IP is put into play, so in this case you can give the option of the IP, but not the CO (I'll concede that I'm unsure if the CO will be negated in FED ball, but I believe it is).