Sundering stuff established in the Q&A

[Cleretic]

Eh, I think it's mostly because ShB is written way before EW. "something not as it seems" is and has always been a thing in ffxiv since it's an on-going story. Just like how hydaelyn "lied" about zodiark back in HW. How the true properties of astral and umbral aether is only known in ShB. How we thought nanamo died in arr, and only revealed to be alive in HW. That's why the encyclopedia of eorzea is even written as "made by the in-game npc" so they could easily retcon or add lore to it.

Actually, we know that Endwalker was largely stencilled out before Shadowbringers launched. We have heard before that they plan two expansions in advance (hence why the clues of the first Sin Eaters turned up in HW's patches), but we've also heard of late that Emet-Selch's presence in Endwalker was written before they knew he'd be as popular as he is. Since he became popular pretty much instantly on Shadowbringers' launch, that says that they knew the real story behind what Emet was telling when he was telling it to us. It's also shown by the fact that our real first foreshadowing about the dynamis stuff was in 5.0, but not in the MSQ; it's in the Dancer questline.

They aren't writing it literally just before producing it, there's a lot of lead time, and they do very little in the way of retconning (unless it's 1.0 stuff). In fact, of the stuff that you mentioned, going by how we know their writing process actually works...

• Heavensward's patches were being written around when Shadowbringers was being planned (again, the Sin Eaters). That means they had the 'Hydaelyn is a primal' reveal figured out at that point, so they knew when she was saying it that it wasn't the whole truth.
• The 'light and dark aether' thing is an interesting thing where it's not an actual story-relevant detail that was 'retconned', but rather a scientific assumption. But when taking into account that those terms initially came up in 1.0, and we do know that they were actively rewriting 1.0's lore details (Thancred's Japanese VA accidentally revealed to us that when he was cast the Ascians had a different backstory), and then adding in that 'planned two expansions in advance' thing... yeah, this one probably was a retcon, but it's not exactly a big one. This didn't change anything at all.
• Nanamo's 'death' was literally during the Heavensward leadup (HW had been announced for five months at the time), they absolutely didn't write the Parting Glass with the notion that she'd stay dead, because they were producing those cutscenes and HW at the same time.
• I don't think the Encyclopedia Eorzea is written in-universe to protect them in case of retcons; it's there to protect us from spoilers (and also because it makes for a more interesting read). Consider that when volume 2 was written, it had a section on the Warriors of Darkness when Shadowbringers was in production; they didn't make the section without that information because they were still deciding it, they did it because they wanted us to find it all out in-game.