I'm not sure if this is what you meant, but I guess one thing I would suggest is having a character on the show that was aware of the same things that the audience up to date is as well that would address the rest of the things time traveling involved in Endgame that didn't bleed into Loki. But you've been of the sentiment that Endgame's time travel plot has nothing to do with Loki's so I would think you would find that unnecessary.
Still, I disagree with the rest of your post and I think we should agree to disagree because I really just cannot agree. If pruning a branched timeline means erasing it, then there 100% is a conflict with Steve returning the stones because that means it is impossible for him to return the stones if the timelines where those stones came from are erased. For all I know, the TVA's erasure of the timelines if that's even what pruning the timeline means could be simultaneous to Steve's returning of them the "moment after they were taken," but I'll never see a conclusion to that because the show just didn't address it.
I didn't see Steve's mission actually pan out, nor did I see the effects of an entire universe erased with a time resetter. But from the beginning I never thought that's what the TVA does; I just didn't think about it too much at all. And by the end it is easy to let it all go by subscribing to the idea that it is what Kang wanted.
I just can't wrap my head around why you think erasure means would be impossible to return the stones. He returned them immediately after they were taken... which is obviously BEFORE the TVA arrived. This obliterates your "conflict" regardless of whichever definition of pruning you subscribe to.
Endgame's plot leads into Loki's plot, but that doesn't mean Loki needs to retread Endgames plot. Steve returning the stones is immaterial to anything that happened in the Loki show. Why didn't "Loki" explain what happened to Gamora? The same reason they didn't talk about Steve returning stones. Because it's immaterial to the story at hand.
The show did have characters who knew about everything that took place after 2012... but those characters only talked about things pertinent to Loki's arc... which naturally doesnt include Steve or the returning of the stones.
The entirety of your argument is "i imagined this cannon-conflicting scenario, and the show didn't explicitly tell me that it didn't happen". But simply accepting the cannon means the thing you dreamt didn't happen.
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