This is where it gets heated, and in my opinion it does and doesn't fix the problem.
What it does fix - You're getting rid of all the algae, and all the tank water and dead algae in the cooking vat either has or turns into organic waste that breaks down through the cycle. Because there is live rock in there and you aren't "feeding" the vat any extra food or organics, the rocks and water in the vat will eventually reach 0 ppm nitrate, nitrite, and ammonia. That is great for everyone, but what about the tank itself?
What it doesn't fix - If you still have the tank running, and you are still doing the process that introduced all the nitrates and phophates in the first place that the algae was growing off of, then once you put the rock back in there, you will grow algae again on your newly cooked live rock. So, in order to make sure that your rock stays "clean", while it is cooking, you need to do proper tank maintenance such as reduce bioload, reduce feedings, waterchanges, etc, etc. i wouldn't even put rock back in it until the tank itself has 0 nitrates and phophates.
I don't follow any rock cooking threads or anything like that. I have just read enough to get the basic concept of why people do it. But, reefpod, that is a very good question. And that is my "logical" answer. So, technically if you go back before cooking the rock basic, simple, and responsible reefkeeping techniques could have prevented this in the first place or even if you started responsible techniques after a problem has occured, then you would have eventually narrowed it down and fixed it anyways. But yet i understand that sometimes, things call for drastic measures. I would just say cook the rock in emergencies only instead of for aesthetic appeal.
I'm definitely not saying that it doesn't work, because logically it does. But what is the point of going through months of no rock for a little algae? Now if your tank was green with hair algae from top to bottom, nitrates at 150+ ppm, and 5 phosphates, then you either need to take down your tank and start over, cook your rocks, or enjoy a "Planted Marine Tank"

But in my honest opinion, nothing will ever beat responsible techniques. And because of these techniques is what makes Bare Bottom tanks work. But that is another story....and lets just not go there. That would be thread piracy :lmao: