Hi kljr, I have been reading chinese forums for some time. They have huge experience on snapping turtles. I have found out that they call this situation fading, as it happens in flowerhorns.
Basically, turtle looses the skin which covers bonny shell scutes. They say that the reason is low ph, dirty water and one-way feeding.
They suggest keeping the water alkaline, full water change once or twice a week, and feeding variety food. They also say that commercial turtle food is bad for their carapace and they must be fed on live or frozen fish and only a little turtle food.
Also they say, the shell will return back to normal, if all the requirements done and provided a good amount of UVB. But it will take a very long time, may be years.
I have the same problem with my ally snappers, I noticed the problem started when I used too much wood in my setup and it gets worse when I delay water changes. One of my affected turtles recovered in 6 months, but the other 2 got worse.
I had the information about the reason and solution only a week ago, so I am not sure if the suggested treatment will work.
i went though my snapper staying out of water, ecen though it was crystal clear, i did a total water change and immediately within 2 minutes he was back in water. The fb group is all snapper owners 
