Just because a team wins, it does not automatically make the protest null and void (at least I don't think it does.)
It's just usually assumed that the winning team won't actually file the protest. Since the team whose protest came first won the game, if they don't file their protest, the protest committee would only have the second protest to consider, and if upheld, the game would resume in the 7th inning.
If the winning team went ahead and filed their protest, the PC would have to consider that one as well and if upheld, the game would restart from the 3rd inning.
That's my opinion anyway.
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