Is your MSFS bought from Steam or MS Store?
The bindings should not be wiped out. I’m wondering if there is some type of syncing issue with the cloud. Steam does this differently than the MS Store version and the location of these files on your PC is different between versions.
See this topic about location of the folder where these settings are stored (MS Store & Steam):
https://forums.flightsimulator.com/t/joystick-profile-location-steam/362631