GJB,
Why do you think the saltwater has anything to do with what you are seeing? Soft stone will erode from water in general, the amount of salt in a saltwater pool will make little difference.
You can't hurt anything by trying to seal it, but I have my doubts that it will do much good. My daughter has flagstone around her pool. Her flagstone was flaking long before it became a saltwater pool. Since becoming a SWCG pool, nothing seems to have changed. The flaky stones are still flaking and the non-flaky stones are still not flaking.
I would not stop using the SWCG, as I don't think that is the source of the problem.
Thanks for posting and maybe we'll here from some members that have used a sealer..
Jim R.