What renamed atlas?
Doing it as you suggest doesn't change anything I'm getting.
Let's see if I have this right:
Reference atlas is blank - it's just a state, points to whatever atlas you assign to it. It works, but it doesn't switch between the two other atlas's sprites, which leads me to:
The sprite names aren't the same between HD and SD, as they're suffixed _HD / _SD - are you saying they have to be named the same?
I'm not sure if my NGUI install is even working properly. If I change the ref atlas Atlas Type to Reference, then click away and click back, it returns to Normal.
No doubt I have something all wrong in my head - is there no documentation for the UI (not just classes)?