I have been suffering from keybinding loss every bloody time I exit the game. I finally got fed up of it, and started messing around with files.
From what I've figured out, the game does not care which bindings you customise, and loads the default file anyway (There are multiple binding files). The solution is to edit the default binding file, and use ; to comment out a binding, or change the key/s to your liking. Obviously, do not comment keys which you need.
Default file: \steamapps\common\ARK\ShooterGame\Config\DefaultInput.ini
Other binding files which the game ignores: C:\SteamGames\steamapps\common\ARK\ShooterGame\Saved\Config\ (There are 3 folders here, each having a DefaultInput.ini
Enjoy.