I have a flood and drain system that I am going to be using Coco Coir in and I was going to be adding in beneficial bacteria. But after seeing your results in my cloner and the explosion of clean white roots I have to conclude that chlorine is good for the plants root system.
If I were to use chlorine with a dead-res in flood & drain, I'd choose an inert media like perlite. With organic matter such as coco, the chlorine will be quickly consumed since it will react with the growing media.