I am sorry mere if I came across sounding like you are not taking care of the seahorses as a priority. I did not mean to imply that at all.
I can tell from your many posts that you are doing all you can to save them and to get their tank to be a healthy enviroment. I applaud you because I know it requires a lot of work. I also know how stressful it is. Hang in there my friend.
Without photos of your tank it is going to be difficult for me to see if there are areas prone to collecting debris. However if you keep up your maintenance in the tank without ponies, the water quality is bound to be much improved in 2-3 weeks. The water changes will be lowering the DOC and also the bacteria count should go down if there isn't anything to keep feeding the bacteria. Adding a probiotic or even just seachem stability will help establish good bacterias instead of pathogenic bacteria.
It is possible that your coral were indeed reacting to cleaner water. As a rule coral do not like changes so keep an eye on them as you continue to maintenance the tank. I can not remember if your fish are in QT also. If they are not sick it might be best to keep them in the display tank to produce a small steady bioload for the coral.
How are the seahorses doing in the QT? Are they eating ok?