Ah, I get it now. Yes, definitely bypass (I would remove it completely if possible) the heater. However, before you drain and acid wash, I'd at least try shocking the water for an extended amount of time first, and you might even try rubbing a vit. c tablet on the stain just to see if it will come off with ascorbic acid. Won't cost much to try....

I can't imagine what the other pool service did chemically to cause this to happen in a 3 year old heater. could you please post your water test results....CL, CYA, pH, TA, CA?

Janet