Yesterday Rf2 did not start showing that error message,some Json files are empty. Is that a bug ? In fact deleting that files in the player directory solve it, but annoying that all setups are lost. Maybe it will be useful to make copys from time to time.
backing up your controller profiles is a good plan for the future. Probably also have backups of your player.json so you can re-edit the new one if you have changed some of the settings.