Autopilot and Joystick relationship questions

Please tag your post with #pc and/or #xbox.

Are you on Steam or Microsoft Store version?

Are you using Developer Mode or made changes in it?

Brief description of the issue:
I find the interaction between the joystick and the autopilot often confusing and wish I knew more about how the functioning of the both of them is programmed? I have had long periods where the joystick and autopilot work as intended for all the aircraft I fly. Then suddenly, the joystick and autopilot fails to function properly when flying certain aircraft but not all of them. Checking my joystick function separately in the control panel shows it working perfectly but it will not control flying certain aircraft. I have had lots of problems with the PMDG DC6 autopilot control. My Coronado Piper aircraft now goes into flying circles disregarding of what I do when using the autopilot. These problems surely spoils my enjoyment of flying. From a programming viewpoint, I wonder how the joystick, the autopilot and the actual movements of the primary flight controls are interrelated? Do I perhaps have to empty my Community folder and reinstall my third party aircraft to fix such problems? I would hate to reinstall the MSFS2020 program.