I'm sure it will happen as he builds the next couple of chapters, then a final continuity polish at the end of season one. I think right now, he's just been focusing on getting the story clearly away from the danger territory. My guess is he'll extend the changes to SG S1 with pure script rewrites for simple changes, because there won't need to be many, if at all, but he might simply for clarity, then make sure of all the changes in S2Ch1, then go back and polish Ch1-4 WiaB while doing Ch5.
I think I'm enjoy this a lot more, I like this kind of tension more than the way it was before.
That seems legit to me, not to set him and Miru apart so much as neutralise his potential chaos. At the moment the Zanes don't have any family to accuse of the interference, and Leia's the one who will get the family and the Asanos in trouble. So by Willi returning he's now in a precarious situation where he has to face judgment... but who got Leia to call William back? Emilio and Riri. What's their stake? And who is the mole the fed's have at Leia's? Riri or Emilio spring to mind. But it could be any of the girls, that would be easiest.
They're the ones Kata mentions at the farm in ch3