New scene loads and I no longer have any controller input

My guess is that your OVRinputManager got destroyed from one scene to the next - and then it is trying to be referenced for the controllers but is now void/null.  You might be able to fix it by re instantiating this when the new scene loads up.  I know that was a vague answer, the docs are here - https://developer.oculus.com/documentation/unity/latest/concepts/unity-ovrinput/