Yeah the script Vig pointed out works wonders. I had some issues when modeling some HP rock objects in ZBrush. They were instanced and randomly rotated/positioned on a mesh for baking, but some of them became inverted from some random transforms issue. The script saved me tons of time doing them one at a time :)
There is a great little script that helps unify the normals and flip faces. This saves you from having to run around the mesh and flip each face and you never really know if you got them all when you do them one at a time, this takes care of it and points them all in one direction.…