I will throw my .02 in if that is ok. I would suggest you replace it all at once! Let me explain this while you pick your jaw up off the floor! Lol if it was me I would cycle all the new rock in a tub,use an enzyme like enzyme 9. Do water changes the whole nine yards! When your seeing good levels and hopefully some purple stuff set up a QT and transfer everything you want to keep into the QT. ! Then save a small amount of your present sand. Remove the infested rock and sand from your tank and do your thing. Use the small amount of old sand to seed your new sand bed! Once you get the sand,rock scape and new water in add the enzyme additive and cycle the tank. You know the rest. You need to replace the sand as well as the rock to lose the mushrooms.Well that was more like .03 but any way that is what I would do. Good luck. Or you can do your new build then transfer it then. You need to PM me an e mail so I can scan the drawings and send them to ya! I am almost done with them and your new cube is going to be sweet!