I'm having a similar problem. A custom world cell that has mountain peaks that I deleted long ago and yet there in game, but in CK there know where to be founded. I can't see them I can't select them or move them around there just not there. I run DynDoLod and that can't find the meshes either because DynDoLod won't generate LOD for those mountains there just not present in the CK, but there in game and they won't go away! It doesn't matter how many times I open up and close the CK. It doesn't matter how many times I refresh the window use wireframe, or starting a new game or cleaning the plugin with tes5edit. I've even gone in game and wrote down the object ID to look for them in CK, and I can't find away to search for an object ID in a large cell. If some one could give us some leads that would be helpful.