The reason: Plot & Script.

To answer the question about why they returned Mjolnier.

If Cap never returns it, then Malekith of the new timeline will have the upper hand on Thor, and conquer the nine realms.

Thor took Mjølnir to the present day because he has a strong connection to that hammer, he basically loves that hammer.

And about the Ancient One and the flow of reality: I guess that what she said was only in theory, she never experienced such thing before. Or maybe it takes a loooooot of time to reality starts becoming strange. In IW it was only like 1 minute or less. In Endgame maybe the flow of time and the reality stuff was having consequences but only not happening on Earth. ¯\_(ツ)_/¯

I imagine it’s impossible to fully destroy an Infinity Stone.

Law of Conservation of Energy - energy can neither be destroyed nor created, and both Doctor Strange and Agents of S.H.I.E.L.D. have proven there is no breaking this law.

The energy of the stones must have simply been dispersed across many, many particles, so they still remain in the timeline, but across many small particles.

I think he took it because they were going to replace everything/erase the timelines anyway, so he just thought "Why not?", he wanted to see if he was still worthy and wanted a bit more time with it.

And they returned it just in case that was necessary.

The writers have said though that it likely wasn't necessary to return it.

*Jeff Goldsmith: "What would you tell the people asking about where Thor's hammer, Mjolnir, is?"

*Stephen McFeely: "I think he brought it back to Asgard."

*Christopher Markus: "He gave it back to the Thor of that time."

*Stephen McFeely: "Which was actually probably unnecessary if you take the stone because you're going to erase that time - that branch where he doesn't have it anyway."

And yeah, the Russos and one of the writers have pointed out that Thanos says the stones were "reduced to atoms". As close to "destroyed" as you can get, but not quite. Likely the same with Wanda destroying the Mind Stone. Destroy the physical stone, but its essence still exists somewhat, just is unusable.

The only way an Infinity Stone can actually be removed is plucking it out of the timeline.

Thor removed Mjolnir from that timeline because he is an imbecile. He thought nothing wrong could happen. I'm pretty sure, the other Avengers were like: "Dude! You can't do that. How is the 2013 Thor going to fight Malekith now?". And then Thor would say: "Oh well, that's a good point.". When Bruce Banner informs they need to retrieve the stones back to the moments they were taken out, there is a chance to retrieve Mjolnir back as well. It seems Mjolnir was useful in 2023 anyways.

And... both Scarlet and Thanos destroyed the infinity stones, but the energy of these still remains, scattered across the universe. The energy of the stones its just not contained in stone form, but it still remains so that the universe doesn't fall apart. Removing a stone from a timeline is removing that whole energy and that is why the universe might fall apart in that specific scenario.

This is overthinking at its finest and I love it