Not sure what you mean by lag.
I went back to the Pyramid to make sure I had tripped all flags, and it turned out that even though I had beaten the boss, I didn't turn on the green crystal next to her. So turning that on resolved that flag. But I've gone back to the boss room in the Royal City Sewers multiple times and found the green crystal glowing as if it was activated, and I am unable to interact with it. I've completed the rest of the seemingly important quests in the city post-demon, too, such as the Pregnancy Wave and having Damia come personally to the Royal City. All the while, no changes by the boathouse to Amazon Isle--still given the same "we've gotta wait for the storm to pass" line.