I had a similar instance, bbut mine was just the hot side (no anode in the water heater) I drained the system. Added bleach to the fresh water holding tank and filled it. Used the pump to fill the water heater, and open all the faucets until you smell the bleach. Let the water heat up, then open a hot faucet and let it run until cold water comes out (turn of the water heater while doing this part) then turn the water heater back on, let it heat up and drain it again. I then ran the fresh tank (with bleach) through the faucets until it was empty. Hooked back up the water supply and havent had an issue since.