My first thought about this is regarding polishing SS versions of the watch ... does it possibly degrade the seal that make is water resistant?
That shouldn’t even be a possibility. If you’re using the Cape Cod cloth and lightly applying to the scratched casing, your cloth shouldn’t be coming anywhere near the ports. Plus, that means that some of the solution would actually have to somehow make its way in between the casing and display or inside the ports, which I find to be _very_ unlikely.