Rinsing won’t remove Po4. Gfo or lanthanum chloride will without taking out the rock.
“Waste” will make nitrates no3. You can reduce that with organic carbon dosing and beef up the bacterial Biofilter.
If you redo the rock work on established tank. , drain the water down till the fish are easy to catch. And pull out the rock.
It’s easier to replace sand, but rinse with water and light peroxide till it’s clear and put it back in.
Sensitive corals may not like it.
Stirring up the sand bed will stir up some nasty stuff. I don’t reccomend doing that with fish and corals in the tank.