Running a phosphate reactor or phosphate media will not kill chaeto.Light,organic waste,nitrates is used by chaeto as well.I know of nothing killing chaeto except maybe a cycling system.
Appreciate the feedback guys. I can't seem to find out why but I have seen some chaeto die off in my sump. Nothing has changed in the tank.
I've had this happen and heard that it can happen - for a variety of reasons - it can happen to all sorts of algae.
The problem is that as it dies it releases everything back into the water and can almost trigger a cycle-like blip in nitrites etc.. so you might want to pull it out of there. This is what I have ended up doing in the past - I take it out, pull it apart to break out some healthy looking pieces, then throw them back into the sump: they always seem to grow back into a healthy mass.
If your water isn't very good then you might kill your chaeto, but I run a low nutrient SPS tank with very low phosphates and organics and my chaeto doesn't have any problems. If you are running so low on nutrients that you kill your chaeto then you are going to kill all your coral as well.
Well I took out all the rock this past weekend. It was breaking down and falling apart. The rock I used was not what is found in normal saltwater aquarium. It was free and tried it out and it did not work. Will try something else later.