Freshwater dip recovery?

Hi guys
I had a threadfin butterfly with what I suspect was Gill flukes. I've been treating with prazipro and it didnt seem to help as much, so then I started doing paraguard, but today I noticed he had blotchy spots on his tail, so I thought it was about time for a freshwater dip to get rid if the nasties inside his gills. I dipped for 11 mins 30 sec, he was laying down the first minute but when I nudged him he got up and was swimming the entire time. Now, a few hours after he's hiding and still breathing even harder than before (his gills were opened farther in the first place due to the flukes). So my question is, is this normal and will he return to normal breathing in time? Or are the flukes still there and he's sill breathing hard because of them? Thanks!

Also! I saw a few small worms in the bucket along with a bunch of flakey things that looked like dead skin, the worms I know we're flukes, but what about the flakes?