The Witcher 3 installs now (through gog client) a dxgi.dll, overwriting the one installed by the mediator / reshade client. Problem is that reshade then of course doesn't work. Removing the d3d11.dll and renaming reshade64.dll to d3d11.dll makes it work again. However the mediator didn't do this. Not sure if this is hardcoded, but it's perhaps worth looking into. (as in: if there's already a dxgi.dll, delete d3d11.dll and rename to that dll instead). Game didn't run when I tossed out dxgi.dll it installed by itself and replaced it with reshade64.dll.
Just a FYI for the people who run into this same issue