As the setting is several hundred years after the various games I've run in it (about a thousand after the first game), and many of the characters are long lives - some have survived.
Ari is still in the Dungeon of Sephiroth. The dungeon has to be there, it was there before there were Gods. Basically because it was used to create Gods in the first place. A bunch of bored mages got together and thought "let's study where magic comes from", "I know, lets construct a ley line chanelling building that will allow us to tune our subconscious to the use of magic properly", "Gee - what a neat idea", "Dear me, you seem to have achieved Godhood - how inconvenient", "That hardly seems fair - let's take turns", "Okay".
Although technically people worshipped gods before there were Gods - they just were never manifest, and had no sentients. Bit like today :)
Nadia is still around, and Gwen. They're not speaking. Gwen stayed a God, but the Mage and the Dwarf are gone (the Dwarf went home down the Daemon Cleft).
Then we have The Weeping Prince and The Great Dragon. Always looking for adventurers to undo what they have done. Kinda difficult to get people to change history back to the way it should be and cause themselves to never have existed...
At least The Great Dragon has a hobby now - sending terrorists to Zylistan.
The Seer and the Sorceress are around. He gave her a stiff talking too and she's no longer achieving godhood by herself (hey, she was bored).
All of these NPCs are basically Powers in the world. Should the PCs ever encounter them - the suggested course of action is to be polite, nod and smile, and seek a safe continent somewhere for a few days.
But it should make things interesting when we eventually play...