Dropped third strike...and then some!

[Spookyant]

Tough question for you, sirs:

Junior Division: Runner on second, first base unoccupied, two out, home team at bat, and the visiting team is ahead by one run in the bottom of the 6th inning.

Strike three is called by the umpire, catcher makes the catch with "webbing down" in the dirt. Umpire calls strike three, but does not announce batter is out or call game. All players leave the field to begin post-game congratulations.

The last batter removes his helmet and abandons his bat to join team in congrats to visiting team. (Batter does not enter dugout/bench area). Home teams' manager suddenly tells batter to put helmet back on and run to first. Confused, the batter does so, and continues running bases after prompts from his team to continue. Visiting team is instructed by their manager to ignore this event and focus on his post-game celebratory words. The batter/runner stops at third, removes his helmet and finishes the teams' game ending ceremonies. Home team manager files a protest, claiming the catcher dropped the ball, which is upheld by Umpire-In-Chief. The managers' evidence was that he saw the ball rolling toward the mound at the games' end. The catcher claims to have thrown the ball back to the pitcher. Pitcher claims to have given the ball to the first base ump who rolled the ball to the mound. First base ump supports this claim when asked by Umpire-In-Chief.

Days later, the decision is reached granting the batter in question first base, and the runner from second is GIVEN HOME PLATE! The score is now TIED as the game is restarted from that point.

On what grounds does the runner receive the right to score? Wouldn't said runner be forced to return to second at games' restart? Could visiting team appeal that runner abandoned, or that batter/runner passed preceding runner on the bases when he continued past first? So many questions in this one...

Thank you for your help!!