Yeah, Gamora got rebooted to the beginning of Guardians 1. If she had gotten dusted, Nebula would know, and also if Tony dusted "everyone that came with Thanos" then Nebula would be dusted too.
Black Widow is gone "for good" because her future is now in the soul stone and time flows through the infinity stones. Pulling her out would be like pulling the stone out of the timestream and would create one of those really dark F'd up timelines that The Ancient One warned Hulk about. Gamora on the other hand is not connected to the stones, she's just a random thing from the past, like Mjolnir or Thanos' army. They don't mess up the time stream of the MCU if they don't go back, because time doesn't flow through them because they aren't infinity stones.
Now, Cap can return the soul stone just like any other. Even if Red Skull can't put it back in the sky (no rule says he can't, btw), worse case scenario, Red Skull just holds the stone in his hand. Boom. Timeline still has a soul stone, no broken timeline.