Having experienced a velvet outbreak 2 years ago, in my tank anyway, it only effected the fish. It did kill 3, 2 were treated and are still with me today and 3 did not show any signs at all. All the survivors were transfered into a temporary tank while my display remained fishless for 12 weeks. In those 12 weeks, I began working on the invert side of things. Collecting mostly SPS corals along with a few LPS here and there. All snails, crabs, shrimp and every inhabitant on and in my live rock were good. After the 12 weeks the fish went back in and everything has been fine since. So to answer your question, your coral should be ok. If it was me, I'd leave it in the display while the velvet runs its course.
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