Leave the skimmer off for as long as the directions say. Chemi Clean works wonders. Sometimes the chemi clean stays in your water for a while and when this happens, I have to end up changing my water. I would let the skimmer go crazy and dump out all the wet skimmate out and then replace with new saltwater. Its a bit tedious, but it works for me.
Also, try not to leave your skimmer off for too long. A skimmer is a great resource for providing O2 to your tank which affects a lot of things like your PH levels. Make sure you keep all water params in check during this process.