Remove /region remove <id> <priority> /region rem <id> <priority> /region delete <id> <priority> /region del <id> <priority> Removes a region. Something like that? Picked up from wiki here.
You could make another region inside it, allow everyone to build/destroy it, and just make it a higher priority than the larger region? I don't think its possible to delete a small section of a region.
You make a new region inside your big region, and flag the abilities for people to be able to build and such.