protest play???

[wentdl]

Runner on 2nd base 2 outs, batter is called out at 1st but runner on second rounds third and trots across the plate. Offensive coach calls for appeal on runner at first saying firstbaseman had foot off the bag. Base ump confirs with plate ump whom then reverses the call, runner safe at first and ALSO allowed the run from third to score. Now the protest is more centered on the fact the run was allowed to count,HOWEVER, the play started with an appeal on a judgement call.

How far do you peel this onion if it gets peeled at all. Is the run allowed to score because the umpire jeopordized the situation with incorrect call on judgement play??????