Delete all the region files and let them regenerate? The world.dat file contains the seed, so the generated nether should be the same, but empty.
zolteex You could just rename it and it would have the same effect as deleting it since it wouldn't be able to find it, and thus would regenerate a new one.
Super User Can you even read what the OP said? He wants his nether world to regenerate, not to choose an area and regen it...
Yes I read it, a lot of people don't know about the //regen command. Also if you would of read my post you would see "if you want".
I see "If you want", but this might not even be helping his problem. A world and a region are two very different things. He clearly wanted to regen the world, not a region.