Deleting Layers

Looking into this further, I copied a layer, I decided I didnt want that layer anymore, so I deleted all takeoff and annotations from the newly created layer, there were overlays also, what I found out, that even if takeoff and annotations are deleted, it still thinks there is something there because of the overlays, if I delete the overlay from the layer, it deletes it on all layers. Can it be fixed so that it does not look at the overlays as a takeoff or annotation item so that unused layers can be deleted.