Funny that this was updated after 5 years - was looking through posts about this because this essentially just happened to me too. Not to mention,
@Knapp870 's scenario was just like mine, in that I used chemi-clean a few years ago with ZERO problems. It did just what I wanted to, no side effects.
Since my house move / tank move, some cyano resurfaced again. I grabbed the SAME box of chemi-clean. Checked for an expiration date, didn't see any. Figured it should be good to go. Threw the dose in there, at about 80% of the recommendation, and turned off the skimmer, just like I did the first time and per melev's advice. After a day and a half or so, tissues from my LPS were literally flying off. Every single coral in the tank looked miserable, and with multiple head losses for most LPS. Just like Knapp, fish and inverts were totally unaffected. Worst of all, this time, it had almost no effect on the cyano.
Just did a 30G water change, turned back on the skimmer, and will probably do another 30G change tomorrow. Accepting that probably most of those LPS are gone, which sucks, because I already didn't have many coral in the tank to begin with. Seems like the common denominator here might be an old batch? I'd suggest for people to make sure you get a new box.