both teams lose track of outs

[Steelers]

Hey guys
Had a situation late this summer. Not sure I handled it correctly, never had this happen before. HS BB game late in game. During a long 7 or 8 run inning with a couple pitching changes. Bases loaded no outs batter hits into 6-4-3 dp. BOTH teams believe it is 3 outs, both teams vacate the field, I look at the HPU gesture "I've only got 2" and he agrees. Score keepers realize that there are only 2 outs. Now here come the managers...... Defense wants R2 out for vacating, Offense says R2 rounded 3rd and scored and wants the run. So we put R2 on 3rd and put the defense back on field. Do you guys agree or is there a rule that would govern such a situation? I have had one or the other forget outs but never everyone on both teams

Steelers