Games are played under protest all the time. The only time the protest is upheld is if there is a black and white technicality. I don't believer I have ever seen a game replayed due to a missed call.
There's no way they replay this game based on that. if that became a precedent for replaying games the season would literally never end.
<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">Dallas Keuchel's 2016 season debut: 7 IP, 2 R (both earned), 3 H, 4 BB, 5 SO. 106 pitches, 62 strikes. Retired the last 11 batters he faced</p>— Jake Kaplan (@jakemkaplan) <a href="https://twitter.com/jakemkaplan/status/717442452647452674">April 5, 2016</a></blockquote> <script async src="//platform.twitter.com/widgets.js" charset="utf-8"></script>
There would definitely have been an upheld protest a few years ago when Porter was managing against the Angels. He brought in a relief pitcher. The other team pinch hit. Porter removed the relief pitcher without him facing a batter. That is a blatant violation of the rules. Somehow Porter got the umpires to agree with him. Soscia was livid and played the game under protest. The Angels came back to win so they withdrew the protest. MLB subsequently suspended the umpires for a couple of games due to not applying the rule.