DISCUS dark not eating + white cotton in tank

Question
I have a 36 gallon bowfront, 3 (give or take) 4" discus, 3 (give or take) 2 1/2" discus are the  main inhabitants. Also 10 small cardinal tetras, 1 4" ghost knifefish (previously a rainbow shark and clown loach, please read on).  Tank is established been running 6 months. ammonia is low (light green in tests, trying to fight it down with prime and water changes, seem to remain in light green), 0 nitrites, low nitrates, ph is 6/6.5 temp 84.  

Things started going wonky when two of my bigger discus paired and started laying eggs, at the time I didn't have a second tank to make a breeding tank... never really planned on this, but thought it'd be fun to try, I put up a tank divider and gave the two their own little space, they laid eggs 3 times, the eggs would get fungus so I made the mistake of buying methylene blue and dumping some in the tank, mind you this made the WHOLE tank blue. I then read it destroys your good bacteria, so maybe 5 minutes after dosing the tank I pulled out all the media filter and put in secondary media filter.... days later it didn't seem to work in saving the eggs and I began cycling it out of the tank. The divider remained in the tank and the all the fish on one side flourished and the pair on their side remained a healthy couple for several weeks. It is now over a month later, I removed the divider from the tank to give up on hatching fry, since then I have put the original filter media back in, done a lot of water changes (2, 3 times a week, at 30% - 40%) bought a bio orb bag to help clean up, I've been watching everything water parameters seem ok.

BUT after I removed the tank divider one of the paired discus began acting REALLY strange. Once the strongest discus in the tank.... now got dark in color and eyes dark as well, it previously was the tank's largest and dominant fish, always floating in front, mediating the others and really vibrant looking. It hasn't eaten anything in maybe 3 weeks (I've fed sinking pellets, frozen beef heart, frozen blood worms, dry brine shrimp) he looks at it but doesn't eat it, everyone else eats as normal. During feeding he may come out of his corner and he watches me... he may nip at another fish.. but then returns to his corner. I've doubled up on vacuuming the tank and making sure to do a 40% water change at least once every 3 days, but I've noticed small cotton balls floating in the tank, and it grew a few times on some of the air lines as well (since has mostly stopped on the air lines). During this time I had two other fish that died, one was a clown loach, the other was a rainbow shark, the shark I found hiding upside down in a cave with small growing cotton balls on his gills, I treated him in a small hospital tank with melafix, cotton balls went away he began swimming right up but then died after 8 days, the clown loach went lethargic and upside down (had no cotton balls) and was put in the hospital tank and died two days later. the loach went into the hospital tank with the already 4 days dosed melafix and one water changed water, so that might have been a shock I don't know.

My main concern is the discus not eating. The cotton balls I keep vacuuming out and staying on top of. but the discus don't seem to have any cotton balls on them or deteriating look, aside from the one discus not eating and being dark and unsocial and in the corner. I'm really worried he's definitely going to die unless he begins eating. I'm scared of putting him in the hospital tank because so far everything I put in there has died.

Hospital tank and main tank are at 84 degrees. I water change with a proper dose of prime, I now water change with prime and a cap or two of stress coat. I also bought Pimafix seeing that the melafix I administered to the hospital tank and main tank hasn't helped anyone or got the main discus out of his funk. I don't want to put pimafix in the main tank in fear of destroying bennificial bacteria.

I don't know what to do, besides continuing my water changes, getting rid of any cotton balls I see, I scrub the plants in the water from the water change before putting them back in, and I clean the gravel really well.  the tank has all artificial plants, I rearrange them to give them new territories in hopes of encouragement of the main discus to retake his colors and throne, other fish seem to be really happy in the tank, nobody bothers anyone. There was a brief week during this time of one other discus slamming himself into the tank walls which I never experienced in the past, he has since stopped that, never lost his colors as well as eating normally. it's just the one main discus who before was the head hancho, and now looks lost in the corner.


What should I do? he's not going to eat anything. He's gone long enough without eating, something needs to be done =( I used a big turkey like baster to put the food in his direction, I wish I could just shoot it in his mouth!! If I put him in the hospital tank (has not cycled, I keep water changing, 0 ammonia, 0 nitrate, 0 nitrite, same PH and heat as main tank, hospital tank is bare bottom, community tank has gravel I routinely clean) with pimafix, I feel like he will die =(  

but if I need to put the heat up to 90, or administer the pimafix, the hospital tank is where it should be done, I don't want anyone else effected.

thanks in advance sorry for writing so much, I kind of hold out until the last minute to do something when it's finally out of my hands, all your help is really appreciated.

JC

Answer
JC, it sounds like you are taking the proper care of your tanks. Remember though that adding new filter media kinda starts the cycle over in a way. The beneficial bacteria live in the filter media as well as throughout the water and thrive off of the stuff the filter catches. Once new media is introduced, the bacteria has to grow on it before it can be established. I assume that the water is soft for your discus, this is a requirement to keep them. The fry feed ofl of the parent mucus, but it sounds as if there is a bacteria in the tank. I have the best results in treating and curing fish diseases by using Mardel's Maracyn, Maracyn 2, copersafe, etc. These are the best in my experience and I wont go with any other type. I would give it a try. You dont have to remove carbon from the filter and it WILL NOT destroy your biological filter process. Other than that, you are doing a great job. What I do for my hospital tank is, I keep one small freshwater fish in it to maintain the safe and constant process of the biological filtration that should take place in an aquarium. This way it is always a safe healthy "hospital" tank. I hope this has helped. Good luck, sorry for delayed response. Feel free to contact me in the future. One thing I want to add is that, more commonly, fish stop eating and slow in activity when the nitrite levels are unsafe. You say it is a safe range so all the more reason to believe that there is a bacteria in the water. Most fish can adapt to environments that are out of their normal habitat. It is better that all parameters are kept stable than a fluctuating rise and fall of the water quality with attempting to raise or lower a level.