As long as you are going to break down your main tank, let me suggest the following procedure which will help removed adsorbed metals, and persistant organic chemicals.
Once you have removed everything from your system (all critters and substrate), but still have the pumps and such hooked up.
First, disconnect the plumbing to the refugium and isolate it from the rest of the system. Do not reconnect it until you have finished the procedure below.
Caution: Be very careful with both the acid and the bleach these are hazardous chemicals. Wear rubber gloves and disposable clothes...
NEVER allow the acid and bleach to mix, if you do, you will generate chlorine gas and this will ruin your whole day - and your lungs.....
Open some windows and make sure the room is well ventilated and then...
Go to your local hardware store and get a gallon of muriatic acid. Fill the tank half way, and then add the gallon of acid to the water. Fill the tank the rest of the way. Turn on the pumps and let the system circulate for a couple of hours. This acid bath will dissolve any adsorbed metals from the system. Then drain the tank of all the acidified water (it is safe to go down the drain). Fill the tank with fresh water and let it circulate for an hour or so, drain again. Fill the tank a third time, and add a gallon or two of bleach. Let it circulate for a couple of hours. This will remove any organic build up. Drain this solution out. Then fill and circulate the tank with fresh water and a super dose of dechlorinator. Drain this again. Dry the inside of the tank. If the tank smells of bleach repeat the last rinse.
At the end of this procedure your tank should be free of any contaminants.