Jon - I would personally try to rid the Cyano from my refugia. Just my opinion though, and from my experience - Cyano is not an algae and the bacteria is of course alive in the main tank. Also, I've never read(other than maybe conchs) or had great experience with any invert eating Cyano.
Marcus makes a good point. To answer Jon's question, I will speak from personal experience. If it gets worse than I can stand, like it's covering everything, then I siphon some of it out and swish it around as well, but I don't do a water change. I hate to bother with a water change when cyano is the way that nature handles an increase of nutients. After all, it's a bacteria and algae combination! It's eating the nutrients before the sand bed can get any. I guess now that I think of it that way, removing it is being kind to my favorite sandbed. So who should I favor? That's a question of personal taste and probably doesn't matter in the long run. As I siphon it out, I know that nutrients are being removed from the system. Hmmmm, one of the four purposes of the refugia! On the other hand, I've often seen cyano disappear after a few days or weeks as other processes recover/step up to handle the nutrient load.
About two months ago I posted a pic of some bright green cyano growing on some of the back sand in the Bangerter 180. It's been there for about a year and doesn't get any worse. I kind of like the color and I definitely like algae...so it stays and causes no problem!
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