I have been reading on a couple of occasions, that people attributed shell rot to too high moisture in the substrate. I really wonder though, if that is the case, especially with regard to redfoots.
In literature about redfoots in the wild, K. Moscovits f.i. writes, that she observed redfoots in Maraca using burrows, that got flooded in the rainy season as well as after any harder rain. So they were basically sitting in water puddles, keeping cooler and well hydrated that way. When these puddles started to dry out the tortoises covered themselves with the resulting mud.
So this does not sound as if keeping them on moist substrate should harm them.
The exception might be, when a shell injury is existing. In that case high moisture would likely support the growth of fungus and bacteria. But I doubt, that all your redfoots, that are concerned, had plastron injuries to start with?
I really hope, that you can find out from somebody knowledgeable, what is causing the problem, and what can be done to treat / prevend it. As many of us are not blessed with good reptile vets, the more we can find out ourselves the better.
Ed,- why do you think, that a mite could be the problem? I thought, that mites attack through the skin of reptiles?
And what did you do with your animals, that were affected? Did you treat them or did the problem resolve itself?
Gaby