What effect does it have though?
Surely the input folder has nothing to do with it, maybe the net code or others.
If you lost your controller configs, just go to your aircraft, click on the controller column, then load config, and go to the renamed folder input folder, and select the input controller config for that you want to input. :)
I wonder though if this will still be broken method if they have now changed modifiers etc?
I'll test later tonite anyway after loading up fresh 1.2.6 install.