True the bacteria deep inside the rock will survive, but it will be affected. This will reduce your filtering capacity, causing your cycle. Plus all the critters your fish and coral feed on will definatly be gone. You could also leave your rock in the dark for a few days. Alot of the algea will detach and the stuff that is left will take a while to get going. maybe giving your refuge a chance to take the lead over your HA. Let us know how everything goes.
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Current tank: 120g 30g fuge 2x400w MH 220VHO
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