the only thing i can think of now is that the file(s) that holds the details of your controllers and/or mappings has somehow become corrupt.
I’m afraid I didn’t know what they were called, but the good news is that i found this while i was searching, New computer new Windows 10, new MSFS2020 install crash to desktop with USB joysticks plugged in - Self-Service / Peripherals - Microsoft Flight Simulator Forums.
I know it’s a Steam installation and yours might not be, but it would seem to suggest that renaming/removing the controller configuration file(s) might do the trick and I am sure that you can find the MS Store equivalents of the files the OP identifies in his own solution.
Good luck