Make sure you have all your original controllers connected. If something is missing (or if something new has been added) then the game sees it as a new setup, hence why your custom binds might have been overwritten.
try this
remove(bad) binding folder from its default location sling it on your desktop for now so it is no longer in the correct dir (this can be deleted later)
restart the game this will create a new default binding folder (close game)
now grab the good old backed up files and sling them into the new folder overwriting(or deleting) whats there but b4 you do rename your good old bind files
instructions on how to do this here in post 5's three steps https://forums.frontier.co.uk/threa...t-every-time-i-enter-the-controls-tab.507856/