ive recently had a similar experience with a colony of zoas/palys from cuba, the polyps slowly stopped opening and then they just browned and died/rotted away, this all happened with a new colony i purchased that had not been placed in my tank but went straight in a QT after a 10 min fresh water dip (as everything does) very odd as nothing could be seen on the exterior of the polyps, my next step was to remove and seperate ALL polyps to see if the spread due to all connected/growing from the matting. again the dieing continued so i then cut open the some dieing polyps that were not quite rotted away and found tiny worms, so not sure if they moved in to eat the dieing/dead flesh of polyp i cut open some seemingly unaffected polyps that were still opening every day and to my amazement again found tiny worms within the flesh.
so this i presume was the culprit and every single polyp has now died.
the worms were pinky and around 5mm long and thin as a needle, the curious thing was they swam like in a flowing ribbon fassion, when i first found these inside some dead polyps i thought they were just baby bristle or eunice worms but these took out the colony, so i guess this colony had eggs deposited either on the polyps or matting that burrowed within without leaving any signs of entering or the eggs were injected by the parent in the first place before i purchased.
