Unfortunately I never played FFXI, so that section of the multiverse is out of my grasp. Only other world restored to it's "true form" I can think of is Final Fantasy V, and I've brought that up before. Suffice to say, while it was a massive event, and Bartz and co. were absolutely certain it was evil due to the cacklings of the root-mustache-twirler who planned it, the event itself proved relatively benign, and Exdeath's true evil plan simply required that event to take place.

Going totally off the rails, to the point that I can't possibly be right at all and should just copyright this now for later use. I wonder if, rather than the "original form" being all life reduced to the orange Tang of oneness (dammit, Gendo), there might exist some essential other half to every being that is kept separate by the nature of the universe. If something were to happen to one of the two halves, it might reflect on the other in some way, perhaps altering the boundaries of their soul. We gained the Echo when our other half died, and Darklander gained his when the 1.0 posterboy died at Cartenau. There could be Chrono Cross logic at work. This might also be why the Ascians that are "of this world" can materialize freely, while those that are not require a vessel.

I say this because I don't think it's going to be as simple as dark==nothingness. It can, sure, in any other system, but as Moose pointed out about Astral and Umbral, Umbral isn't "nothing" so much as an inversion: the equal but opposite force. We've been beaten over the head with the possibility that another world exists out there, tied to ours. There may be some fundamental difficulty with coexistence, and there are certainly conceptual issues that would arise when the light and dark halves of a being merged, but travel between them seems to be possible in enough of a capacity that I don't think it's a nonworld that nonexists out there so much as a substantial other side of the coin.