Oh hai,
I'm running a 40Slot tekkit server (tekkit.endetgaming.net). We are using the //regen command of worldedit, too. It regenerates the area as is was is most cases. I only got some weird generation near water areas.
Another con of this command is that you should be carefull with any Redpower2 stuff and the Chestmod Chests around the area to regenerate. The regen command clears the ModChests with no way to reroll it. Redpower2 wireing will disappear, too.
This error doesn't seem to be only in the chunks of the regenerated area. I experienced it crosschunk.
So whenever i use the //regen command i ask the player if any RP2 or Modchest blocks are around and tell him about this error.
I don't kow if its just the //regen command or Worldedit in general having issues with those mods. But never saw any similar problems with other worldedit commands.
Best regards
Jojo
www.endetgaming.net