The Org members become complete humans again after their Heartless & Nobody forms are both beaten. Not really all that horrible a concept considering how Heartless & Nobodies are born in the first place.Wait that's how the Organization members come back? That's incredibly stupid. And really....time-travel? Is that what DDD is about? I'm in for some bullshit...
And the time-travel is more about Xehanort kind of picking up all his different forms from different points of time to gather in the now for the final clash between the 13 darknesses & 7 lights, less about just flying through time will-nilly. It has some pretty strict limitations & rules.