Oky-doky here are a couple of spots to check. OBR 7.10 (at least in my BR Book that is where it is. pg 75.) "Appeal plays may require the umpire to recognize an apparent 'fourth out'. If the third out is made during a play in which an appeal play is sustained on another runner the appeal play takes precedence..."
So in your situation. R2 R3 B/R missing first base. If the defense appeals quickly enough (ie before B/R returns to bag) this would in essence become the 4th out and cancel the run scored by R3 OBR 4.09 (a) Exception clause.
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Ty
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