With the time travel theme Marvel uses in his own way the M-theory, the Multivere theory. In this M-theory, every smallest change in time gives rise to different timelines and with that to different universes. The Marvel Comics have been using this M-theory for decades and in the MCU it was first teased or introduced with Doctor Strange. So, according to Murphy's Law, everything that can happen happens. This is not new in Marvel and so all rumors, that Disney would destroy Marvel with this time travel case, is not true.
In Infinity War, Doctor Strange also addresses it briefly. The 14,000,604 possible events and future events he sees are all possible timelines that could be caused by an event from the past. These are all possible time lines in which the Avengers could lose incredibly often. This also would mean, that all 14,000,604 possibilies would make 14,000,604 different timelines and so different universes. But that did not happen.
This also means that not only one universe can exist, but that there could be unbelievably many next to each other, but for Doctor Strange only one thing came into question, namely the one in which they are with their timeline and how they can stop the snap, or can make it reverse.
But due to the time travel of the Avengers five more timelines emerged beside the main timeline, because the Avengers traveled to five different times. That created five more universes and in total there are now 6 universes with the main one. So far we know, maybe there are more which are not adressed until yet.
And here I go again to the beginning. Many people say that the stones of the main timeline are gone now and so they fall into darkness and chaos, because Thanos says at the beginning of Endgame that he pulverized the stones. But what did we learn from Thanos? He didn't destroy them, he pulverized them only, so i think that they are only reduced into their atoms. So the singularities as such are still there, but not in crystalline form. So a being with enough technical means or enough power could reunite these atoms and connect them to the stones.
But now we come to the very last point that also confused me first at the end of the movie. I had to think about it a bit until I understood it. It's a thoughtful ending, which many people don't see that way. But this only becomes clear when you know some extra things, like the disappearance of the Infinity Stones from the timeline and the bringing back of the Infinity Stones doesn't undo it, and that this acting emerges new timeline and universes.
Captain America travels back to bring all the stones back to the timelines and ends up dancing with the love of his life, Peggy Carter, whom he then marries. He leads his life to what Tony has always advised him to do and can then fulfill his promise to Peggy Carter. Some criticize here things like Cap can't undo everything the Avengers have done through their time travel. But that's not what Cap is about. He doesn't even think about it. None of the Avengers think about that. It's about the stones being in their timelines where they were taken, not how they get there and where they are put there. It's only about the stones arriving again at this moment, not how. It is not about transforming the past back into the main timeline and that is no longer possible because what has happened has happened.
It's just that these timelines are not thrown into chaos because one of the stones is missing there. The beings from these timelines also need the stones to protect themselves against the evil cosmic powerful beings and to keep everything in balance.
source This graphic, created by a fan, explains/shows time travel in the MCU best
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