Heaven is still quite large and with the Unconquered Sun gone it's no longer very high on their priorities. The initial flood was largely to keep support from spilling out onto Creation, since then Yu-Shan is something of a resistance city. Demon patrols wander through here and there, and resisting gods/elementals/exalts hide within the city where they can.
Luna is still at large, along with at least two of the Maidens.
There's a few holdouts in creation too, but they're people who mostly keep to themselves unless bothered (Raksi for example). The Underworld is really the only unified front, but the Yozis show little interest in going there.