I'd do it all at once, providing you have enough LR to compensate for the amount of bacteria you're going to remove. You might have to watch the levels for a week or two afterwards (the tank may go through a 'mini cycle').
It might be a messier job than you expect, CC can hold a lot of detritus. I'd probably remove as much water as possible, then remove the fish, corals and rock and put them in holding tubs with heat and circulation. When you remove the CC, the remaining water will probably end up full of detritus, I'd remove it and toss it. Then replace the rockwork, add the sand, fill the tank (consider the water used to replace the discarded bit a water change) and check the parameters. Once you're satisfied the temperature, pH etc. are fine, add the corals and fish and you're done.
Someone who has actually gone through the process of replacing CC may have a better idea. Minus removing CC, the above is what I did when switching from BB back to sand - I removed everything and threw out the last bit of water because it was full of detritus from disturbing the rockwork.