Instancing of objects can be used to aid scene management by further reducing the amount of data in a scene. For example, if a street scene is to be filled with streetlights, the streetlight file can be referenced in once and then the remaining streetlights instanced. If the streetlight file is unloaded, all the streetlights in the scene will disappear because of their instancing relationship to the original streetlight file.
If you have a reference file and instance an object within it and then later remove the reference file, both versions of the objects will be removed in the parent scene. A transform node will be left behind in the parent scene for the instance. This node remains in case other changes have been applied to the instance by the user in the parent scene.
Do not rename a node or change a hierarchy in a referenced file if the parent scene contains objects that are instanced. Such a change will make the instance disappear; Maya will be looking for an object that no longer exists. Maya’s instancing is name-based. By renaming the object in the reference file, you make the original go away such that the parent scene can no longer find it.