The Infinity Stones weren't destroyed, only reduced to their atoms, and so everything carries on as it did before the events of Avengers: Endgame, nothing has changed.
Natasha: Where are the stones?
Thanos: Gone. Reduced to atoms.
Bruce: You used them two days ago!
Thanos: I used the stones to destroy the stones. It nearly... killed me. But the work is done. it always will be. I am inevitable.
If we take the second thing Thanos says as literal, whereas I don't think it is, and the Stones are destroyed then the following is my speculation.
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:
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.
Time is strictly set on the "main" timeline: There are no Infinity Stones left and so you can't create an alternate reality.
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.