Recycling your rock will not necessarily kill of what ever is in there.
I would put it in some salt water in the dark for a few months. It will kill off pretty much whatever needs food to survive. After the problems you have had I would be careful to add your rock back into the tank. That or trap whatever you have in your rocks.
You could keep them in fresh water for a bit and see what comes out.
My rock was dead for two years and it comes back alive fast if you add some starter rock.
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150 Gal system 3'x3' 400W M/H, Bekett skimmer, Dart return,1/4 HP Chiller
180 Gal Drop tank, LED lights, Bubble master 250 skimmer,Hammerhead on a closed loop, Speed wave return.
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