It's a mess and one group or the other will be ticked off whatever is done to try to fix it. I'm no umpire, but I believe one would have to stick by the rule as much as possible rather than try to discern what is most fair. If runners advanced in the chaos, you can't put them back. If runners are thrown out, they are out.
Part of it is knowing the rule whether it is verbalized during the play or not.
Again, an embarrassing mess when it happens.
Well the rule actually does specify that you are allowed to call an infield fly after the play is over. You are then by the rules allowed to rectify the situation as you have probably placed one team or the other in jeopardy.
You certainly wouldnt keep outs if you decided that the play should have been an infield fly and runners get thrown out because they didnt run and stayed on the base.