This thread was started out of concern for your corals and has somewhat side-tracked. Pics of your corals, or at the very least, a proper desrption of their behavior would sure help us out in trying to trouble shoot your problem.
Should I remove carbon before adding Chemi Clean? The Whisper will not take it out will it (other than the carbon)?
Remove all froms of chemical filtration, including carbon. Filter pads, if just floss, can remain. If you have a skimmer turn it off.