I have gotten this process tuned and dialed in over my time in this hobby. So this is based on my experience.
When I started out I factored in most cost effective method while still maintaining and transferring all that beneficial bacteria from the old established bed for minimal interruptions in waste management. When I started there was no bacteria in a bottle. If you didn't know someone that could give you some seeded bed you were out of luck and had to wait. As a benefit if done this way the explosion of new populations of beneficial bacteria and food web\ organic processes based off the old colonies is fast and starts processing waste fast. Allowing for minimal downtime of nutrient management and helps stop or slow an algae outbreak/ mini cycle that commonly happens with new substrate. You help stop that initial spike in your numbers.
I usually use a large portion of the water when doing stuff like this. I take what I want out before making any changes in the tank. I place the water in storage containers with a heater and source of water movement like an air stone or powerhead. That way I get the water particulate free as possible. But still get aged salt water. I used about 100 gallons of my 180 setting up the 225 and the rest new saltwater.
To be honest I have read a lot of the PO4 bonding issue and have read both sides (yes and no) and I am on the fence for it as a large source of it. I think it is given more credit then it should. I myself have not experienced this issue. Anytime I thought I had it turned out it wasn't and the issue was caused by other factors. Like laziness on my part.
What most likely happens based on my experience are the organics themselves get trapped in the rock\ substrate and fill up all the little holes. Then they break down contributing to nutrient load. Especially if they aren't rinsed and cleaned before storage. What does leach out are the organics themselves that are causing the PO4 issues in the first place. Poor tank husbandry, over stocking of systems, over feeding and poor nutrient export are the bigger contributor of nutrient issues I would think and not PO4 leaching from rocks. If you lock that stuff down you limit the PO4 in the first place. (personal opinion)
Up till my 225 build I used the same crushed coral bed for over 20 years having no issues. The only time I started to get issues was at the end when I had to replace before the 225 buikd. In time it got so old it started to break down into small particles turning areas to muck and started to bond together under the low flow areas like rocks and form something that was like concrete. I have also been using all the same rocks for decades with no issues. I just bleach them before drying and storing and clean them before they go into the tank. If the PO4 leaching was large source of PO4 I would have ran into the issue by now.
If moving tanks I want to reuse the substrate as much as possible. I scoop off the top portion of substrate a few inches down and put into a container and not rinse.(keep an airstone and heater as it will consume o2 fast and you get die off) I then take out the lower portions and put small portions in 5 gallon pails and rinse in aged saltwater. To much in the bucket doesn't give you a good clean and to little is time consuming. So I do under half pail at a time. Then add to tank or other storage container. I stir up using my hand till it looks pretty clean as I keep dumping water out from the top. Or just rinse under freshwater with the tap running slowly to help dilute if you don't want to use aged saltwater. I keep the first layer unprocessed because I want to maintain the beneficial bacteria and food web that lives in the substrate and get rid of the organics by washing the rest of the bed.
If you want toss out the bottom layer or rinse in freshwater till the brown color comes out. That is where the anaerobic and anoxic zones happen and will have the most sludge buildup. You can't get the water to run clean as the freshwater dissolves the outer layer causing cloudiness due to the PH. So don't bother trying. Mostly clean works. Then just do partial water changes over the next few weeks to deal with anything that got stirred up.
I add new substrate if I choose to at this time on the bottom layer of the tank (can mix with the old washed) and put the unprocessed top layer that I saved on top again. I add some new on the top as well to give it a little prettying up. Using the old helps stop that ugly diatom bloom that happens on the new crushed coral as it already has the bacteria and micro fauna to deal with it.
You also get a faster seed of the substrate bed by inoculating it with bacteria and micro fauna for the food web\ organic processes doing it this way. If you want add the beneficial bacteria in one of the products you can get nowadays. I like reusing the bed as I like to be cost effective. Blasting through products adds up fast in the hobby. I would rather spend the money on a new coral or new hardware.
