Well, since you are focused primarily on CH you should know that I use four CH controllers for AH. I also have a locomotive controller (http://www.raildriver.com/products/raildriver.php) for my nephews to use, and two Xbox Windows controllers for my wife's side-scrolling games. If I log into AH without first remembering to check for the presence of any one of these controllers, then my mappings will be unassociated (usually the views more than anything else, but sometimes axis as well). If you only have time for one flight and this happens, then nothing gets done because you have to first fix the setup. I would think it would be easy to fix by HTC.
I have connected to my computer, CH Combat Stick, CH Pro Pedals, CH Pro Throttle, 2 Xbox gamepads, Logitech G27 Racing Wheel and a Belkin Nostromo and I've never had a problem with the controllers I have not assigned in AH interfering like you've described.
I've also just run a test, I removed all of my controllers (so my CH controllers no longer are assigned to Controller ID# 1-3) and then plugged in my gamepads first (Controller ID# 1-2) then my G27 (Controller ID# 3) then the Nostromo (Controller ID# 4) and then my CH gear (Controller ID# 5-7) and started up AH and sure enough, AH still saw my controllers assigned to my CH gear without me having to reassign my controllers and saved whatever bindings I had mapped to my joystick and throttle.
I then removed my controllers again, assigned my CH gear in mixed order (Combat Stick as ID#1, Nostromo as ID# 2, Pro Pedals as ID# 3, Xbox game pad as ID# 4, G27 as ID# 5, Pro Throttle as ID# 6 and my other Xbox gamepad as ID# 7 and started up AH again. Same result, AH recognized my CH gear without me having to reassign them and saved the mapping I had assigned to my CH gear.
The only thing I had to do was recalibrate my controllers in game but the mappings were saved.
ack-ack
