+1 with what has already been stated but here's what I did with mine, of course what works for one does not mean it will work for you. I left my hippo in the tank, fed frequent smaller feedings (I fed mine 3 x's a day or at least twice) enriched with garlic, put a new algae strip in the tank daily, kept the stress down as much as possible. There's other treatments as well, fresh water dip, hypo salinity but if it were me, that would be my last resort measure. Sometimes moving/catching him again will cause even more problems, additional stress on the fish.
What other fish do you have in the tank? From your pics, it looks like ich on both sides, when you say fungus, can you describe it a little better? Could it be that he has much more Ich on the one side than the other? Has he rubbed himself and now has a sore place?
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