After every update I delete all the Metashaders in the Terrains, then kill off the FXO and another one that I can't think of off the top of my head in the "Saved Games folder.
I have about three or four mods/changes that I have the manually put in. (ALE Flare and Chaff settings, DDI Color and the VR Shaders)
I'll then run the game in VR just to make sure everything synched