I don't know why the CYA would disappear (other than water dilution from rain overflow) over the winter when it was disinfected. If the chlorine and pH levels were high, then the oxidation of CYA by chlorine is faster, but in cold water that shouldn't be very fast. In a pool during the summer the loss is usually around 3 ppm per month while in a hot spa it's around 5 ppm per month.

I don't know what to do about the phosphates. It should get lowered more and maybe if they are released as PoolDoc says then doing another treatment might work, but I'd expect to see it drop soon after treatment and only slowly rise up if in fact the phosphates are "attached" elsewhere. If you had HEDP metal sequestrant in the pool, then chlorine oxidation of it will produce more orthophosphate -- do you have HEDP in the water?