I'm in the process of removing crushed coral like tbar is doing it. I siphon it out weekly during the water change, using a siphon hose, but not the big attachment that vacuums the substrate. When I have most of the cc out, I'll slowly add rinsed sand. I don't think the little bit of cc under the rocks is going to be a problem. I'm not having any problem with nitrates, but the sand will be more attractive and better for the critters that dig in the sand.