You'll only lose photosynthetic organisms such as algae when you cook rock. Everything else stays alive because you're keeping the water heated and circulating.
After cooking my rock there's still an abundance of pods, worms and other critters including fan worms, hydroids, sponges, baby brittle stars etc. There was even a sabon shrimp hitch-hiker that I had never noticed before until I was returning the rock to the display tank and it literally jumped out at me!
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