Not sure why it would clear other than if you were in a different stick mode that you hadnt mapped.....IE bomber gunner mode, Fighter mode and so on.
An easy fix is to copy your controller files from the settings folder to the desktop. Rename them by adding a VR_ in front of each, safe them and drop them back into the settings folder saying yes to the popup "do you want to replace...."
This will give you the same controller settings as the regular 2D version of the game. Once you have a good setup for your controllers make a copy of the VR_ files for your controllers and keep them someplace you can find them so if it happens again, you have a quick replacement setup.