Otdfbt

The Ancient One explains:

"The Infinity Stones create what you experience as the flow of time, remove one of the stones and that flow splits."

As we know, post Avengers: Endgame,

(all instances of) the Infinity Stones are destroyed (see this question: What is the status of the Infinity Stones post Avengers: Endgame?)

What does this mean for the flow of time? In particular,

does this mean the rules of time travel are different in the MCU depending on whether you travel to before the destruction of the stones in 2018, or after?

We don't know, in fact it might not even be different. All we know is that The Ancient One tells us that the Infinity Stones control the flow of time and removing one spawns an alternate reality. This leads us to three possible theories of what can happen post Avengers: Endgame:

1. Time is unregulated: Time is now unregulated and so any number of alternate realities can be created by using the time travel and altering things.




2. Time is strictly set on the "main" timeline: There are no Infinity Stones left and so you can't create an alternate reality.




3. There are 7 realities: the main reality plus six realities where each Infinity Stone was removed (destroyed).

I'm of the opinion that it is probably number 2 as the Infinity Stones were destroyed at the start of the film and so we saw what is apparently only one reality with no others created. However, it is all up in the air until Marvel decide what they are going to do post Endgame and in fact it might play a role in GotG3.

As Josh commented on the question it's also unclear if the Stones were destroyed completely or just reduced to their atoms. If the latter they are still around and everything still works out as The Ancient One expects.

My reading of the movie is that the flow of time is not different at all. The reason for it is something like:

The Avengers travel backwards in time and remove the Infinity stones, spinning off new alternate realities. They bring the stones into the present (5 years post-Thanos) and use them to undo the initial Snap. Then the stones are sent back to their initial times once everything is resolved. The big assumption here is that returning the stones removes the alternate timelines and results in a single timeline that we are familiar with from the movies. This is what Hulk suggests and the fact that the Ancient One goes along with hit seems to lend it some credence.

The above forms a stable timeloop, meaning that everything that happens in the previous MCU movies really did happen. There is a single timeline that includes all of the previous events and at a few points

Future Avengers are acting in the same time/location as their past selves.

The biggest take away from all of this is that

The rules of time travel don't actually change. It would be possible for someone in the main timeline to travel back in time to before the stones were destroyed, steal one of them, and that would spin off a new timeline for the future where the stone was stolen. I would say that time is still regulated in the post-Thanos timeline because the Infinity Stones were destroyed but not actually removed from the universe. Their constituent atoms are still present, unlike in the (temporary) alternate timelines where they were stolen into the future. Even if the stones were completely destroyed I don't think that would actually change the rules around time. Firstly because we can see that timetravel works after they are destroyed, and secondly because if the stones can be used to destroy themselves that feels like another baked-in function of the universe and not something extraneous and weird (like timetravel shenanigans).

According to your Ancient One quote and the corresponding scene, the removal of the infinity stones causes a fracture in the timeline - rather than its destruction. This type of event would be large enough to create a new reality and split the timeline. Bruce's response, however, is that returning the stone in time and place allows it to either merge back into its previous timeline, or it does so functionally because it is an identical copy (nothing has really changed) so that events moving forward are indistinguishable between the two.

The bigger question about fractured timelines comes from

Loki escaping with the Tesseract, Thanos not being around after he brings his army through, and Captain America somehow settling down in the past, where his presence most likely wrecks hell with time in general (although we are supposed to ignore that). All of these create an unstable time loop.

Any of these should result in a fracture, and could possibly result in multiple subsequent fractures. Furthermore, we have no way of knowing whether or not that this was done through the quantum realm previously. Short answer being that the rules of time have not changed, but rather new web of realities have been created.