So when I ran my party through Curse of the Crimson Throne, I also threw in Academy of Secrets, partly because we had a character that was an ex-student Arcanist that had gotten expelled due to reasons and I thought it would be cool to revisit now that the Arcanist had grown in power.
I'm going to move forward assuming GMs or folks that have played AoS and CotCT are reading this...
During AoS, they had confronted Toff Ornelos and ended up fighting him, killing him before he could escape. Upon the conclusion of CotCT, the Arcanist player (well before Shadows at Sundown was ever announced) liked the idea that his character would become the Headmaster of Acadamae and start the rebranding process. This paired with the party creating a Council of different cultural representatives to rule the city.
Even more importantly, at this point the heroes that defeated Illeosa had stymied Lothract's plans twice now (I think at the time with a successful knowledge check, I had let the players know at the end that Illeosa's contract was ultimately held by Lothract and he was not pleased)
Working in the Council instead of Queen Cressida is going to be easy enough, my difficulty arises in replacing Headmaster Toff Ornelos in SaS particularly since part of his motivation is knowing he is just a figurehead.
Would having a Deputy/Assistant Headmaster that is in unwilling service to Lothract (maybe always opposed to the Arcanist's progressive policies) is the one that interacts with the PCs? (Potentially the new Headmaster is down in Absalom visiting the Arcanarium for a symposium or something, getting that high-level PC out of town)
Any other fun thoughts? I've got about 6 months before we get close to me running this, but I know I'll be running it!