Time Travel as a plot device isn't my favourite, for just this reason. There's just way to reconcile it logically.
My understanding is what they established in the movie is that time travel can't change the present. Otherwise, Gamora travelling to the future means she wouldn't be sacrificed for the soul stone, and the future would be completely changed. If that happens, the Snap never happens, so they never travel back in time and she doesn't travel to the future. It's all very paradoxical. It would be like Back to the Future where reality changes around you due to changes someone made in the past.
Instead, it sounds like what happens is that any changes that happen in the timeline create alternative realities. There's a notion in the comics of a multi-verse, where history unfolds in a different way in multiple timelines. The original timeline, however, remains unchanged.
I think, for time travel movies, it's best not to overthink it. Just accept it as an (admittedly) unrealistic plot device, no more or less real than a man who turns into a Hulk.