I'm thinking that you're removing the ecosmarte, right? Treat the pool with a metal sequestering system to remove the copper. DO NOT USE ANY CHLORINE TO SHOCK, YOU WILL STAIN YOUR POOL!
You should also test for copper to ensure the sequestering treatment has removed the copper. Once gone, you can convert to bbb or AutoPilot.
However, if you don't rid the pool of the copper first, the Pool Pilot can introduce enough chlorine to cause the copper to stain your pool too.