What to do?

[Bluefoot]

Originally Posted by mbcrowder

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.