i dont have a CH pro, but i have seen something like this with my joystick
where it would just stop working some times, usually it would come back in a few secs/min - other times it would crash the game (likely because it didnt come back)
my issue turned out to be a bad/loose usb port on my pc case, changed the plug to another usb port and all was fixed
first thing to check is to see if this happens on other aircraft, in my case it was not specific to anything game side
it seems unlikely a specific ‘aircraft’ has issue with a controller since the functions are the same with all of them
(fyi - i fly the xcub most of the time, love that aircraft)