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I experienced a situation where the plate ump did not make it clear to me, the score keeper, that he had called the runner out at 3rd base for leaving too early on a deep sac fly play. There were runners at 2nd and 3rd at the start of this play with 1 out. I scored both runners safe at home not knowing the plate ump's ruling about the runner at 3rd. I continued through the rest of the inning not knowing, and when what I thought was the 2nd out was made, the teams vacated the field knowing it was actually the 3rd out.

I figured out how to edit the game to show the runner who left early as not reaching home, but couldn't figure out how to record the out.

Is there a play choice for leaving early. Meaning, had I known the plate ump's ruling at the time it happened, how would I have scored this?

Thanks a ton for reading my question.

Yes, there is a Left Base Early option for outs for runners.

So, this would be available when I get the typical "what happened to..." prompt?

Yes.