When I had them in my 90 g tank, I did a combination of many things. I raised my PH, I changed carbon frequently, I reduced my photo period, I scrubbed the rocks I did a series of small water changes where I was replacing the Dino-siphoned water with clean water. Shane had me siphoning into a sock when I wasn't throwing away the siphoned water. I fed every three or four days, I did this over a period of time and they began to go away as my nutrient levels went down. I've heard of carbon dosing helping, vodka would be the quickest method. I currently run bio-pellets and haven't had any issues.
I'd hate to kill your rock, scratching the sand will help for sure I think