Hi Carwash,
I know of your dilema.
What is going on is that when you make a map in CH CM then start AH, AH will read the CH map (map is setup in Directx within Windows) which will have all buttons & axis as it read them upon startup. When you assign the map assignments within AH they are saved in the copy of the CH CM map that AH saves within the Settings folder in AH. As long as you don't change the CH CM map within CH CM, all will stay assigned.
But if you change any assignments in the CH CM map & load them into the HOTAS then startup AH, AH will see that the CH CM map has been changed & will then not use the copy of the CH CM map that was previously saved in AH, thus you will have to reassign all ingame settings to the "new" map.
Been there, done that.
What I do now is setup & load a map in CH CM for AH that I will not change, thus AH will not do this to you when it starts up. I then make all "changes" within the game itself which are saved to this map--no more problems.
Look within the Programs/HTC/AH/Settings folder, you should see a file named chcontrolmanagerdevice1.jsm (if you have mapped all your CH controllers as 1 controller--as I have)--you'll see what I'm talking about. Just open it in Notepad. This is the file that AH is using to setup your controllers within the game when AH starts up.
Hope this helps.