Does The Run Count?

[UMPIRELARRY]

This is a 16U Girls Fastpitch Softball Game. Runners on 1B and 3B with one out. Both runner tag up on a flyball, which is caught for the second out. Runner at 3B tags up properly and scores, but runner at 1B leaves too early. SITUATION #1: While ball is live, defense throws ball to 1B ahead of the runner, and the umpire calls runner out for leaving too early. Does the run from 3B count since it scored before the third out was recorded? (i.e. this isn't a force out) SITUATION #2: Defense makes a "dead ball" appeal that runner from 1B left too early, and umpire calls runner out for the third out. Does the run from 3B count since it scored before the third out was called on the appeal? THANKS.