I agree with John - run scores. The appeal of failure to tag up on a caught fly ball is a timing play, not a force play, so the run counts.
Now, if it was R1 on third who left early, and R2 on 2nd who tagged up and scored before the appeal, then the run would NOT count. A following runner's score does not count if the preceeding runner is called out on appeal for the third out.
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Tom
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