The GG on the Shen Hao is mounted from the back of the wood frame (back meaning from the back of the camera, not from the inside of the camera), so its' front surface is pressed against the wood. Therefore, if you put the fresnel in behind it, the GG is still against the wood, meaning that its' position has not changed. If you were to take the GG out, put the fresnel in front of it, and then put the GG back the GG would be shifted backward by the thickness of the fresnel, presumably messing up the focusing to some degree.
It shouldn't matter which side of the fresnel is facing which direction; it's basically a lens, and it directs light the same way regardless which direction it passes through. I'm playing with one of the full page magnifiers here at my desk, projecting an image of the overhead light onto the desk and the only difference I see when I flip it over is that the focal length seems to be a bit shorter on one side than the other.
As fas as I know, all fresnels are made from plastic, so they are prone to scratching (presumably if they were glass you would also have to worry about breaking off the tops of the ridges). Maybe try putting some tape around the bottom of the loupe to give some cushioning?