I shot video of a local comic book convention last week. I did it for my own enjoyment so I didn't have any pressure to produce a professional product, but I had the same situation as you. Some hallways were lit by sunlight from a wall of windows, some by fluorescent lights, some by incandescent lights and the main lobby by a skylight.
I just shot each section separately, adjusting white balance for each area. I don't know if that helps you, but maybe it will spark another idea.