First of all, I'm not trying to enter into an endless debate about the laws of time travel, alternative dimensions, loops or contradicting what Banner or Stark said in the movie about it; but there's one detail you all should have in consideration. One detail that could certainly show us that, because of the Avengers and Thanos' manipulations of the Gems and their time travels, some consequences should happen in the reality of the MCU.
You see, there's one rule about the Infinity Gems that apparently everybody seems to have forgotten. The Infinity Gems certainly are some of the most powerful artifacts in the Marvel Universe, allowing you to control ANYTHING about reality itself. However, the Infinity Gems only work if you are in the same realities those gems came from. This means, if you take the Infinity Gems to the DC's Universe, they won't allow you to affect DC's reality at all. They would be just regular gems. The same thing happens with alternative realities. Each alternative dimension in the Marvel Universe has its own version of the Infinity Gems: Earth-616, Ultimate Universe, House of M, Marvel 2099, Age of Apocalypse... atc. And in each reality, you can only use the Infinity Gems to alter its native reality. In every other reality, the gems are useless. Which means, if you take the Infinity Gems from Earth-616 to the House of M's reality, they will be useless there. Or if you take 2099's Gems to Earth-616, they won't allow you to change reality either. Therefore, if the Avengers were capable to use the Infinity Gems from the past in their present to restore the dusted half of the universe AND destroy Thanos and his army, it means we are talking about the very same reality here; not alternative timelines or whatever.
This means reality should suffer somekind of "adjustment" to keep reality stable after the manipulations of both, the Avengers and Thanos. Remember, Thanos skipped to the future from the first movie of "Guardians of the Galaxy"; which means all his actions from that point to the present should have never happened. And reality should be "adapted" because of that. For example:
- Maybe Thanos never went to Nidavellir to create the original Infinity Gauntlet, so Nidavellir and all the dwarves should be alive and well. Eitri could even still have his hands.
- Thanos wasn't there to destroy Xandar and the Nova Corps, so they should be restored.
- Thanos wasn't there to kill half of the survival Asgardians from Ragnarok, so they should still be alive, including Loki and Heimdall.
- Thanos wasn't there to take the Mind Gem from Vision, so he should be restored too.
- Also, if Cap returned the Infinity Gems back to their proper time once this was all over, when he returned the Soul Gem to Vormir, the deal about "a soul for a sol" should be "inverted", which should restore Natasha back to life.
And there's one final detail. No matter what Thanos said, he may have destroyed the Infinity Gems, but they were just vessels; the inmense power hosted inside of them CAN'T be destroyed. Like science says, "energy can't be destroyed". The power inside the Gems had to be sent somewhere else; and after the Avengers brought the past selves of the Gems to their present, I believe this could cause for the Infinity Gems from the present to be restored by themselves. Like I said, the power HAD to be sent somewhere, and the Gems restoring themselves in the most logical option.
Finally, the Russo's brothers said that, after taking the Soul Gem, Red Skull was freed from his curse, he left Vormir and started his own plans for the stones. That means, somewhere else, Red Skull is back in action, and taking Thanos' torch, he could become the next insane tyrant who wants to exploit the power of the Infinity Gems. And if he's going after the Gems now, it means they should be restored at some point, like I said.