Also another thing you can try is in Rhino delete objects (so you have no objects but maintain the layers, unlike File > New) and use File > Import or Copy/Paste to bring in any objects you edited in MoI rather than using File > Open in Rhino.

You could test that and hopefully what might happen is objects on a layer that matched that name in Rhino would get assigned to that layer with the existing Rhino layer unchanged, but any objects assigned to new layers that you created in MoI would have the new layer created in Rhino for it to go on. I'm not sure if that's how it behaves or not though but it might. If it works like that, then that gives you another way to move stuff back and forth without disturbing your materials assigned by layer.

- Michael