First keep in mind that for games that don’t have a scanner profile specifically tuned for the game, there is a fairly high chance that although the scanner believes it succeeded, it actually failed.
If it actually succeeded and you have DirectVR head tracking, but the gamepad doesn’t work anymore afterwards, try to disconnect/re-connect it. With some luck that might do the trick.
If not you might be able to use vorpX’s gamepad > mouse/kb mapper instead. It can be enabled by changing the ‘Gamepad Override’ option on the ‘Input’ page to ‘Full’. The key mapping is fully configurable. Alternatively you could use your VR controllers in kb/mouse mode, which is more comfortable to use since that way the current keyboard mapping will be visible in the headset on the rendered controllers.