Well since they all reappeared when they did and at that time Traverse Town was still asleep, abandoned of anything aside from Moogles, then where would they go after that? Also, along with that note there's been another question on my mind since Organization XIII first were explained to be Nobodies. What exactly were their Heartless? You'd think people with strong enough hearts to create sentient Nobodies their heartless, like Xehanort, would be superior to normal Heartless.
With this in mind, this would mean that Sora (or King Mickey) has already beaten all of the Organization's Heartless that are present so far since no one but a Keyblade wielder can free a heart properly instead of it just becoming a Heartless again. Does this mean various Heartless bosses you've fought up to now might have been these very Heartless that have now become one with their original self? If so, which one was who's?
And one more point about the Organization, Xigbar (formally Braig) had his space magic powers before he became a Nobody. Up to when BBB came out I thought becoming a Nobody gave them these elemental powers. So then these individuals had these powers all along. All that changed was they had no hearts. Slightly disappointing with how drastically a Heartless changes in power and dangerousness over their original self as first perceived.
"Cogito, ergo es eggo." A.K.A. "I think, therefore you are a waffle."