Looks like Vertex Shading, and if it is, it was there prior to your object deleting. I'm not sure if there are any versions of noggit that can manipulate the Vertex Shading chunk, but i'm pretty sure that's what it is.
So if there were objects on top of these "Blotches" originally, well... you can either put the objects back in or just deal with it if you there isn't a way to remove the shading.