When the Ancient One talked about removing the stones it was clearly in the context of their active use as a defense mechanism (because that's how we know the time stone is going to be used), that their presence is required to be permanent and continuous, and that without them destruction of the universe was inevitable.
They were destroyed so they couldn't be used to undo what Thanos did.
Even within the same movie, the two concepts cannot be reconciled.
The only path to sanity is to treat the Avengers movies as big dumb fanservice and watch the solo movies for actual stories.
(Plus, of course, Endgame ends with Thanos from 5 years ago having been defeated before he could do the snap in the first place or seemingly even plan to do so, creating a grandfather paradox which should cause everything from slightly before Guardians of the Galaxy onwards to never have happened, Sacred Timeline my pasty white arse...)