My experience with Prazi is that it takes a few days to see any significant improvement. The flukes are causing wounds and like with a scratch on you that has turned pink/red, it takes time for the immune system to repair the damage. The flukes, depending on type are live bearers or egg layers. The live flukes are easily killed within a short period of time, but the eggs are immune to treatment and have to hatch out, reason for weekly doses. I am guessing the flukes are probably not affecting the koi any longer, but the damage done could be some time repairing itself and if the fish is severely damaged, may not survive. That may be the reason for the use of antibiotics, the vet saw some serious infection.
Zone 7 A/B
Keep your words sweet. You never know when you may have to eat them.
Richard