Iron in water with stains

The only answer is removing the water containing the metals. As long as you're not adding things to make the issue worse, seems fair to say that you can wait until Fall, let FC fall, add sequestrants and then immediately replace water.
 
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The stains are metal that has fallen out of solution and deposited on your pool surface. When you treat the stains you are putting the metals back into solution so they may be drained out when you replace the water. If you replace the water first then treat the stains you will be putting metal into your fresh water, and may end up with a high enough concentration of metals for the problem to start all over again. It is best to treat the stains first, then drain and refill with metal free water. You can deal with the problem temporarily by using a metal sequestrant until you are ready to drain and refill.
 
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