I'm sure someone will have a pro rule interp book, but I would think that since the game was officially over you could not expect the runners to stay on 1st and 2nd waiting to see if the defense would make an appeal. The appeal (and upholding the appeal) would basically reopen the game and the umpires should simply return the runners to the bases they were on at the time of appeal.
Nothing in the rule book would justify making a runner stay on a base when the game is officially over (by rule the game is officially over when home team scores winning run in bottom of ninth) . Again the proper appeal would simply be a way to reopen the game.
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