I have one tank (well, 2 now) that I dial the wave action down at night, and even turn off one of the lower pumps to, as Brad said, give the fish a chance to sleep a little more peacefully.
In another tank, there is no flow reduction at all, just a lot of holes and calmer water behind the rock work for the fish to sleep.
In all cases the coral is healthy and happy and growing well. So I do not believe flow duration plays much of a part in coral health.
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