nitrates
I say the nitrates did it. 40ppm is alot, over 2 week.s
I have a standard 10gal with a koralina nano and a rio nano skimmer as well, so a bit less flow, and the clown is always swimming, but that's clowns for you (even in th edark). I say al the swimming made it inhale more nitrates? I'd address the nitrates problem, try messing with your skimmer so that it skims more... and do daily water changes until they come in line
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