I sounds like the same thing that is on the pool. I would soak the filter after. What happened is that the some of the stain fell out on the filter - which is what you would want, because then the metal is out of the water. It is hard to do this specifically, but it is a great thing! The reason I would do it afterwards, is that you will probably get some staining on the filter while doing the stain treatment. So it is up to you - you can do it before, but you will probably get some more, so it will be double work. In any case if all of the stain doesn't come off the surface of the pool, let us know.