I'd be giving nothing but a WAG, so I'll have to let the more experienced pros tackle this. But it looks like whatever stuck to the pool bleached it--which shouldn't be a calcium function, I don't think.

Does the liner feel any different there--softer, weaker, thinner? Have you tried rubbing it with Vitamin C, or a weak bleach solution? I'd try that, even using a Borax or Baking soda solution--the WORST is that your liner needs to be replaced anyway. The best is you get it back to true color. The intermediate is the liner is OK but ugly.