only one clown in your 29g tank is probably the problem. a high turnover of nutrients is important for coral nutrition. this means lots of feeding and lots of skimming, and usually other ways of reducing nitrate and/or phosphate. increase your fish load, increase your feeding, and make sure your skimming and nutrient export can handle it. you will surely see some results.
also make sure the lighting is not so strong that they are shrinking away from it. For zoas i like to keep them in as low light as I can, without them stretching towards the light. except for certain varieties that have better color in high light.
honestly you should be glad they haven't disappeared. I had a few frags slowly wither away to nothing from too much light and not enough nutrients (even my sps were all pale) until I figured it out.