If it is ciliates, you may be harming your corals by antibiotic treatment.I share some of your concerns despite reading several reports of cipro dosing not hurting the tank. For now I’m sticking to cipro treatment outside the tank. It will be 3-4 weeks before I get the report back on the bacterial profile of my tank and if it’s relatively normal or atypical. Until I know more (or unless I start losing significantly more coral) I’m going to be very cautious.
I may give a hydrogen peroxide dip a try as well if nothing improves, but i don’t want to do too much at one time. First I need to see if yesterday’s Bayer dip might have made any difference.