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Because the "alternate selves" are from the past. However, this version of time travel seen in Avengers: Endgame (2019) posits that when they travel back in time, they are in fact travelling to a different, parallel dimension. Anything the Avengers do to alter the past in that timeline will not effect their original timeline. The Ancient One didn't want to give Bruce the time stone because she feared it would leave her timeline defenseless. Every event that happened during their time travel would have somewhat altered the future of THAT timeline. Not the original one we've been following since Iron Man (2008) in 2008.

So Thanos wiping out half of all life still happened, Thanos throwing Gamora off the cliff to secure the soul stone still happened, Thor decapitating Thanos still happened.

2014 Thanos brings his armies and his daughters; Gamora and Nebula with him to the 2023 of the main Avengers timeline but again, this is dimensional time travel not linear time travel like in back to the future. So when 2023 Nebula kills 2014 Nebula, she doesn't disappear because this is simply a different Nebula. Likewise, when Tony wipes out 2014 Thanos and his army, he wouldn't have wiped out Gamora because he was aware she was helping them. This Gamora is now stranded in 2023 without having lived the events of the first Guardians of the Galaxy movie. The Gamora that Thanos threw off the cliff in Avengers: Infinity War (2018) is still dead.

The infinity gauntlet with all the stones allow the wielder to pretty much do anything imaginable. Tony used it to wipe out Thanos' army. But even though Tony never met either version of Gamora, he knew she was a member of the Guardians of the Galaxy and that she meant a lot to Peter Quill and the rest of the team. Tony spent a lot of time stranded in space with Nebula. It's entirely possible she told him about Gamora. So when Tony snapped his fingers, he would have specifically chosen to avoid wiping Gamora out with the rest of Thanos' army. Knowing that she became an ally. Much like Nebula.