The .joy file format is simply to provide defaults as a starting point for setting up common hardware. If you are overwriting the .joy file provided by LR, the installer will want to overwrite it for every update. We do not recommend that you overwrite the default .joy files.
If you modify the joystick set up, that will be saved separately in your preferences files and won’t be overwritten.
Note that all joystick files, including preferences, were reset between pb1 & pb2 due to the amount of bug fixes we implemented.