Try what I suggested initially. In your example, you would select the one face that is on uv set 2 and copy it to uv set 1. Edit: Then you can just delete the 2nd set.
By copy are you using copy uv's or copy uv's to uv set. If the latter then yeah it will work with a simple example like that, as far as I know the copy uv's only works on one face. I just tested what you described again it doesn't work in maya 2011, copying one uv set into another stomps the existing uv set. There is no…