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In Avengers: Endgame, in a scene with Bruce Banner and Sorceress Supreme, we learn that the infinity stones create the flow of time and that if any of the stones are removed then they will create an alternate "doomed" timeline. We also learn from Infinity War that the stones were created from the big bang and each control an essential aspect of existence.

So if the stones each control an aspect of existence and can't be removed from a timeline without dire consequences, then how can they be destroyed without the same consequences?

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    Because that was what Thanos wanted to happen (the stones to be destroyed without dooming the universe) when he destroyed them. His second snap (assuming it was indeed a snap) was to remove the stones from existence without damaging the universe, as he was happy with how it was now. Sadly I have nothing that can back this up so I can't really write this as an answer...
    – Dave
    May 3, 2019 at 8:17

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The Russos actually addressed this after I posted this question.

During a Q&A session in Washington, DC shared on Reddit by user zachzhou630, the Endgame directors were asked about the status of the stones and how their destruction affects the time continuity in the main MCU universe. And according to the Russos, the Infinity Stones aren't actually lost: "Thanos only reduced the stones to the atomic level. The stones are still present in the universe."

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One key difference for an in universe explanation. Thanos destroyed the stones by turning them back into atoms. Removing the atoms of the stones from a universe may be what is dangerous. Having the atoms there may be enough to ensure the universe continues.

A more sensible explanation is that Thanos knew of this and when Thanos used the infinity gauntlet to destroy the stones, he also used the power of the gauntlet to prevent the absence of the stones from destroying the universe.

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  • There is actually evidence from statements made by the producers confirming this. If you want to edit your post to include an official statement I'd love to mark it as the correct answer.
    – sanpaco
    May 6, 2019 at 22:29
  • @sanpaco which theory. Also I'm not familiar with official links. If you have official statements, feel free to post your own answer.
    – Goose
    May 6, 2019 at 22:53
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The "doomed" timeline is not inherent to what the stones are, just a likely consequence for them not being present and used to defend the universe. If the Marvel guys don't forget their own statements, we might find out whether a universe without them is truly doomed as the main timeline after endgame now stands without the stones... which would mean, for all we know, the Avengers just doomed everyone. No wonder Cap rather went for a joyride in the past.

That being said, they are not exactly the forces they represent, just a way to manually influence them. Time still exists even when the time stone doesn't. So removing them by itself should not have negative consequences, it just means you lost that tool to influence that universal force. There may be other ways to achieve the same (or similar, like we already saw for the time-stone).

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