If you need a specific Nobody or Heartless (except for bosses) to appear for experience or for synthesis items, simply defeat one batch of them and then proceed to a save point that has access to the World Map and gummi routes. Then, go back to that world (or wherever else you may need to) and all heartless / nobodies will reappear there in their original number.

For example, go to the Proof of Existence save point in The World That Never Was. From there, go to the balcony in The Hall of Empty Melodies where there are some nobodies. Once those are defeated, go back to Proof of Existence and go to the World Map. Then go directly back to the balcony of Hall of Empty Melodies and they will appear there again.