Ok, if you definetely want to keep keybindings and potentially the packages folder (120+Gb) you may be able to backup it and in case it gets wiped, you could restore them to prevent data loss/redownload.
Maybe this helps:
https://flightsimulator.zendesk.com/hc/en-us/articles/360016107019-Microsoft-Store-version-How-to-repair-or-remove-and-do-a-clean-install-of-Microsoft-Flight-Simulator
If you use steam or something else, see https://flightsimulator.zendesk.com/hc/en-us/sections/360003768899-Installation-Guides .
To reset the controller profile I would need to check in the game, but it should be under the option profile manager, where you can also add/duplicate your profiles if I remember correctly.
You can also create a zendesk ticket for official support and raising the issue.