When you assign X-plane commands to joystick/yoke/throttle quadrants it is always a good idea to save the assignments to a new profile using the Manage Profiles button. You then associate that profile with one or more aircrafts. Each time you make a new set of assignments, save them to a different profile. That way, you can have a specific set of command assignments for every different aircraft that you fly.
Each profile will be saved as two files YourProfileName – Joysticks.prf and YourProfileName – Keys.prf in the … X-Plane 12\Output\preferences\control profiles folder.
If you decide to re-download a new virginal copy of X-plane, it’s the easy enough to simply copy the … X-Plane 12\Output\preferences\control profiles folder across to your new installation.
Of course, this folder should always be backed up as well to save you having re-do all your control preferences again.