OK so -resetPrefs worked as intended. It didn't reset the controls but I've set them to what I believe to be the default controls.
Strange that it didn't reset the controls. The settings are stored in the registry in HKCU\Software\ASMB\No Mario's Sky so you could delete that registry key. We'll look into it!
I deleted the registry key and reloaded the game. The controls appear to have reset to default.