No they are not the same. Conditioner takes care of your chlorine etc from tap water. Prime does all that and also bonds ammonia.I have fluval aqua plus water conditioner is that the same thing?
Which corals do you have other than Duncan. One good thing is, Duncan is a indicator coral. If they dont like something in the water quality, they will show that by closing up.
What do you mean by when corals die to they close up? Are you referring to a specific one in your system, its difficult to say how they die without knowing which one.
For example, say LPS coral like frog spawn wont like too much flow and they close up. If we dont move them from that flow, their tissue will separate from the skeleton and die. So it depends.