Just out of curiosoity Bob, when doing your Reality scene for merges, do you actually start the render in Lux? I'm not sure why this makes a difference, but it works for me (read below).

I've noticed that, even if I only make one change with Reality for a lux scene, I need to save it in Studio immediately after as Studio will occasionally forget if I just go off of the scene pre-reality. I normally do this after the export to Lux has completed and Lux is starting up. Close reality, save scene in Studio.

I merge scenes quite often, but then again, I'm still using 4.0.3.47

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