Cooking it should deal with the phosphate/nitrate/etc problems IF, and only if, you do regular water changes while it is being cooked and it is over the course of a few MONTHS.
What you are doing is forcing the nuisance algae to feed off of the available phosphate and nitrate. Over time and water changes you are essentially starving the algae of all nutrients until all the detritus (which is causing the phosphate/nitrate) is sloughed off and removed. The algae is forced to feed exclusively off of the nutrients because you've preventing any light from reaching it.
Make sure you blast the rock will a turkey baster or powerhead when you do water changes and get rid of all the crud that comes off and collects at the bottom of the container.
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