I did some experimenting last night as well. There appears to be no change in surround modes switching between Front A and Front B. Audyessy stays on, and you are right that I will want it disengaged for playback in a completely different room than where its settings were determined.
By pressing Pure Direct, it disables Audyessy. You are right, this is a pain to do every time. In addition, Pure Direct disables all processing. Given that my iPod is a lossy format, I found that use of some of the receiver's processing improved the sound. So now I am looking at quite a bit of fiddling each time I want to switch from HT room to 2 Channel room.
If only Front A and Front B were separately configurable. That would solve the problem and I would only have to toggle back and forth between A and B.
Can anyone think of a simply way to accomplish my goal? And thanks again, Grasshoppers.