What to do?
 

Men's Slow Pitch ASA Championship Game

Top of the Seventh

Team at bat trailing by one run

Bases loaded- No outs

BR hits ball just past pitcher to short stop who is shading second base. SS charges ball. Runner on second holds so as not to get hit by batted ball. Shortstop tags runner, touchs second and fires to first for the force out.
Defensive team mates storm field to celebrate. Runner on third runs through celebrating team to home plate to score. Team at bat appeals play at second
saying runner on second was missed on swipe tag. How would you handle the fact that the defensive team swarmed the field if the appeal is upheld?

They are not making an appeal. They are asking the BU to check with his partner on the call.

If this request for help (not an appeal) is upheld, we have a run scored, 2 outs, a question as to where R2 is placed (probably 3rd), and bring me the next batter.

Why would there be any question as to where to put the runner? The OP does not indicate whether or not the FU called the runner out, only that the defense's bench players swarmed the field thinking that 3 outs had occurred.
If the FU did not call the runner out, then you'd have to count the run scored, or at least award multiple OBS calls on the defense's bench players on the field in the runner's path.

If the FU did signal that the runner was out, then changes the call after conferring with the PU, then there would be an issue of where the runner belongs at the end of the play. But the OP does not state what the FU called.