how often are you doing waterchanges? and what size is the tank and what filtration do you have. The finrot and popeye both sound like a secondary bacterial infection possibly due to poor water quality? Taking out the carbon won't have caused the problem, carbon is used to absorb organics in the water, if you do decide to treat your whole tank (which like discus guru i wouldn't recommend, remove hte discus to a hospital tank) then you will need to keep the carbon out as otherwise the medication will be absorbed by it. Discus lie flat when stressed, so the fact that its lying flat doesn't mean that its past curing. good luck, try the furan-2