He's a puffer , no it won't hurt him as long as there is a slower current somewhere at night for him to rest. My Green Spotted Puffers spend 8 hrs a day on the "Treadmill", and my clowns will spend at least some time there each day.
I wouldn't worry, they seem to practice their moves in the current. If they are paired, the two will also test and practice their coordination in the aquarium (unless they need to guard their safe spot too much to care).
Just wanted to add my new clown experience somewhere.
Got a tank raised occellaris as the second fish in my new 29g. He went absolutely bananas, swimming back and forth back and forth all day and most of the night for four days. Not eating also.
Day five bam! Normal. Chillin out and eating like a pig.
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