water changes are not always a good thing, disease takes hold of a fish under times of stress for example during a water change. 50% once a week is the maximum, if you need to do more than that get a bigger tank and filter because your system cant cope. You need to post parameters such as ammonia nitrite and nitrate (one would assume they would be zero with that many water changes). Also messing with the filters like that is no good either. Only do it when it is a must, that means that when the filter is not pumping properly then it is becoming blocked up and needs to be cleaned. Open it up and only wash the sponges, because that is the only part that reduces flow. Leaving the other filter media alone will leave bacteria in there. After washing a filter out feed the fish as lightly as possible for the next week so that it produces the minimum waste.
What I think happened to your eel is that you removed too much bacteria so there was nothing to remove ammonia, nitrite. Then the bombardment of water changes stressed your fish even more. These two factors allowed the disease to take hold.
Ive found the most effective disease remedies are the ones that are course treatments (ie: add the treatment everyday for a week or whatever). These treatments generally say no water changes during treatment, so the chemical is not being removed from the tank.
If you dont know what the disease is give the fish a general purpose treatment for fungus AND bacteria. waiting to find out exactly what it is could mean the difference between life and death for your fish.