I don't see this as over medicating.  The OP's fish had a clear case of HITH, he treated using the most obvious med for this condition - Metronidazole. He may have used too much at the time, but clearly this wasn't going to resolve itself with just clean water and a good diet. He later discovered worms and dewormed his fish. Again, these worms weren't about to go away on their own.  
Now we have a relapse, bacterial, possibly, something internal? Who knows, often even a vet won't be able to pinpoint a direct cause, unless the fish is dead, and a necropsy is performed.  Souzie could be right in that the pathogen have built  a resistance to Metronidazole, it can happen, and/or it could be this fish is just a genetically weak specimen. That happens too. In the wild it's mother natures way of culling the weak. It's just a guessing game at this point. 
I would still give this fish a break after the Kanaplex, often in groups of clown loaches one will be smaller, runtier looking than the rest.  I have one like that in my group, he's not sick, he's most likely a male, at the bottom of the food chain. Don't let your mind play tricks on you. You were convinced when you got these loaches they were all healthy, from a trusted source. Just my thoughts .....