Valve Index CMDR here, been playing without problems since I got my Index in 2019, using a HOTAS with it. Haven't used the VR controllers in Elite at all though.
Try without the vr controllers? Elite has a tendency to freak out with the bindings if a device included in them is missing, or a new device is introduced to them.
If you have joystick bindings that work outside VR but not in it, it might be the VR controllers interfering with the bindings.
First thing to check is that the bindings aren't set to "empty" once booting into VR.