I've seen that happen with various zoas in my tank. I do have micro stars and pods, but I don't think they are causing the problem. The healthy zoas have stuff crawling all over and around them and they don't shrink back.
I'm wondering if it's some opportunistic pathogen that's causing the problem when conditions are right. I did have one frag close up and shrink after getting hidden under a fox coral for a day. My impression was that the reduced flow led to the problem.
Another thing, which may be just coincidental, is that it seems like this happens shortly after I manually clean algae from the rocks and overflow. I started to wonder if some nasty stuff was coming out of the algae and bothering the zoas.
I've also had thriving zoa colonys shrink back after being fragged.
One thing I've done which seems to help, is to move the zoas to a completely different tank and just leave them alone. I've had several frags/colonies come back after this. The idea is that if it's some kind of microbe causing the problem, then changing the conditions would provide an environment less hospitable for the disease organism.
Here's an interesting one... I had a frag that had been growing very quickly with large polyps and long skirts. One day, it didn't open, an I could see that it had begun to shrink. Some of the polyps had a loose transparent filmy material on them. It was as if the skin was sloughing off.
I put the frag directly in the stream of a powerhead and blasted it for a while before putting it back. Some of the polyps started to open a few hours later.
The next day they were closed again, and I figured I'd try blasting the frag one more time. This time I found a polyp had turned mushy and smelled of decay. I did a 20 minute iodine/SW dip according to the info on ReefFarmers. (I only do FW for nudis)
After the dip, I blasted the frag again. The next day, the polyps were all opened. I've tried the water blasting with 2 or 3 other frags, and it seems to help.
Anyway, the way I'm looking at it for now is that there may be some pathogen that finds the right conditions to spread. It might involve some type of stress on the zoa which lets the disease take hold. Once that happens, the zoa may begin to close up, and deteriorate, decay, or just starve. Changing temperature, flow, alkalinity, pH may help slow the spread of the disease. If the zoa has started to decay, then iodine/SW and or water blasting might help to keep the deterioration from snowballing.
Can people who are seeing this problem try the water blasting or tank change thing and post back if it seems to help?