Be ye warned: HERE BE ENDGAME SPOILERS

I don’t normally do Fridge Logic/plot hole/nitpick posts, and I really think Endgame is a very satisfying movie with good character arcs that basically nails what it wanted to accomplish. All that being said, something just occurred to me that seems kind of significant.
To begin with, I liked the unique take on time travel that Avengers: Endgame uses, before discarding it in the last scene so Cap can farewell Sam.*
But I just realized that there’s another hole in the (mostly) happy ending for the world.** Didn’t we learn in this movie that Infinity Stones were kind of important to maintain the fabric of reality? And there just aren’t any here any more?
Let’s recap: Thanos snapped half of all life out of existence in 2018, and the Avengers catch up to him on his farm planet at some point after that, whether that’s days, weeks, or months later is unclear. In that time, Thanos used the Infinity Stones to destroy the Infinity Stones so that no one could undo his Snap, or whatever reason he had. Anyway, the point is, there are no Infinity Stones in the MCU timeline anymore.
Now, by 2023, the Avengers come back together, figure out time travel, and then hatch a plan to travel back in time, obtain the stones, bring them back to their timeline, and undo the Snap without undoing the 5 intervening years.
They execute said plan, and when Professor Hulk goes to the Sanctum Sanctorum in NYC in 2012, he finds The Ancient One guarding the Time Stone, and she introduces what sounds like a big wrinkle to their plan: the Infinity Stones aren’t just McGuffins with a couple of cool powers either individually or collectively, they are a fundamental part of a timeline’s very existence, and removing one will have dire consequences. Bruce Banner’s ghost properly thinks 4-dimensionally when he says that they will just return the stones to the exact moment they were removed, problem solved. And that’s the mission that Cap embarks on at the very end of the movie; returning the borrowed Stones (and Mjolnir) to the timestreams they came from before anyone misses them. But doesn’t that leave the MCU’s primary timeline, uh, Infinity Stone-less and therefore in some kind of trouble?
Specifically, The Ancient One says:
“The infinity stones create what you experience as the flow of time. Remove one of the stones, and that flow splits. Now this may benefit your reality. But my new one, not so much. In this new branch reality, without our chief weapon against the forces of darkness, our world would be overrun: millions would suffer.”
OK, the last sentence there indicates that the stakes aren’t as big as she otherwise makes it out to be: the Infinity Stones (or just the specific Time Stone she flings away in her illustrative illusion) is “our chief weapon against the forces of darkness,” and missing it for specific uses of the Stones’ powers would suck. Certainly, if Dormammu successfully destroys Earth because there is no Time Stone in that timestream’s 2017, millions is quite a lowball number for how many would suffer.
But the rest of her statement indicate it’s a lot bigger deal than just that: specifically that the infinity stones create the flow of time. So what does that mean for the primary MCU timestream, which, after Cap leaves to return the borrowed Infinity Stones to all the streams they came from, no longer has the things that create the flow of time? Is the flow of time in the prime timestream altered now? It doesn’t seem to have had any effect in the 5 years between Infinity War and Endgame: the world is a sad place because of the Snap, but it’s not like the space-time continuum is falling apart. Or is that what Captain Marvel is dealing with for most of the time the rest of the crew are doing the main plot?
The movie doesn’t suggest that, so I guess the evidence indicates that the infinity stones are not necessary to the flow of time, and TAO was just wrong, or maybe embellishing a little? That doesn’t seem right either; I think we’re meant to take TAO’s wisdom seriously here. Bruce certainly does.
So is the universe actually due to end because we’re out of Infinity Stones now? That seems like a pretty huge question that someone should clarify with Dr. Strange:
Professor Hulk: Oh, bee-tee-dubs, I ran into your predecessor, as I guess you already know, or foresaw, or something. Anyways, she mentioned something about the infinity stones generating the flow of time. Is that gonna be a problem, y’know, without any?
Dr. Strange: What The Ancient One didn’t realize is that the universe sensed Thanos’ quest for the Stones and actually created a back-up stabilizing force throughout the entire universe.
PH: No kidding? What’s that?
DS: Quippy protagonists.

*As the film makes clear several times early on, time travel is not like Back to the Future where there is a single timestream that you can exit, re-enter in the past, and change the present you exited from. Rather, there are multiple parallel timestreams, each self-contained, so when you time travel, you are actually just jumping into a neighboring stream; therefore, whatever you do doesn’t affect the stream you came from, just that separate stream. So Cap jumping back in time to live a life with Peggy is all well and good, but he would not be living that life in the same timestream he left Sam, Bucky, and Bruce in in 2023, and could not show up on the bench there. (Unless that’s some other timestream’s Cap who did the same thing and jumped into their timestream, which means there’s a cascade of Avengers jumping from each timestream to borrow Infinity Stones from others and put them back, etc., etc. Of course, as per the usual rules, the movie didn’t suggest that, it suggests that Old Man Cap on the bench is our Cap). And if Cap can jump back into his own past and affect the future by being on that bench, what does that indicate about Loki getting away with the Tesseract?
Also: Sam and Bucky turn to see Old Man Cap, and Bucky is just like, “Yeah, Sam, you should go talk to him, not me, we’re not close at all.” I get it, I know it’s because Falcon becomes the next Cap, but I think there’s definitely a better way to show that passing of the torch.
**Besides, of course, the fact that all of Spider-Man’s important teenage relations were both dusted and then restored to teenager-hood so that the relationships developed in the first movie are still ready to be developed in the second.