Why would you swap controls to your controller? Can you not just bind the controller to the things you need it for in the same profile with the HOTAS?
I have alternate bindings for my CH setup for trade and for exploration - can switch the control bindings in-game with no issues. I also have a bindings file for using a Logitech stick instead of my CH Figherstick (still use the CH throttle) for RES stuff at CGs (I dont do combat otherwise) - I can plug in the logitech and switch control profiles all in-game. So I don't think there is a bug in the game but I run windo$e 7 and I know w10 had issues over USB devices - maybe that's a problem for some.