Deleting the region fileregion file should force the game to regenerate the chunks when they are entered.
Region files are located in a subfolder of the world directory called "region", and have names in the form r.x.z.mcr, where x and z are the region's coordinates. The coordinates for the region a chunk belongs to can be found by taking the floor of the chunk coordinates divided by 32.
You can also use World Edit's //regen command to regenerate specific areas of the map.