I wouldn't try to save all of the water, I would replace much of it with new water.
You will probably have to do this again in a few days since your are replacing your substrate. Keep a close eye on ammonia an nitrate for the first couple weeks. I would also feed a bit less then usual. I might even skip feedings for the first few days.
After you take out the cc, then put in the rock, then put in the sand, then put in the water. Once it clears out some then put in the corals/fish. It might take a day for the tank to clear.
I scrape coraline often too, sign of a healthy system or not, I like my backround to be unspotted. I scrape it at least once a month. Some spots that require moving more then one or two rocks do get neglected.
HTH