I may be in the minority here, but my experience is that gradually changing from CC (Crushed Coral) substrate to a DSB (Deep Sand Bed) could not be simpler. No need to drain the tank or remove anything, except maybe for moving the fan worms to higher ground during "construction."
Detailed instructions for the changeover are below, but first one vital caveat: if your crushed coral bed is deeper than about an inch, there is some small but finite possibility that disturbing it may release poisonous decay byproducts into the tank and wipe it out. Any scent of rotten egg smell in the substrate is a warning sign, but such a smell need not be present for there to be a problem. (By the way, this would be a concern even if you decided to just scoop out the CC all at once.)
Decide carefully first if you choose to risk this. The alternative is to break down the tank, replace the substrate, and change all the water.
If you want to proceed, do the following. Get a vinyl one-inch bore siphon hose, some "oolitic" aragonite "sugar" sand, a plastic kitchen funnel, and some rigid airline tube that is a snug fit on the funnel outlet and long enough to reach the bottom of the tank.
The idea is to work in small areas, giving things a day or a week or a month as you choose between sections. It doesn't matter, but more time between sections is safer and will let any life in the CC migrate into the new DSB as you go. There is no rush.
Siphon out a small strip of your crushed coral three or four inches wide. (Almost all CC of reasonable size can be siphoned through a inch-bore hose -- if the tank empties too much, just keep putting the siphoned-out water back, using tank water or new salt water to prime the hose.) You can leave the CC under the live rock alone, or lift out one piece of rock each "session" and do under it.
With the CC removed from the small area you are working in this session, put the new sugar sand into the funnel and use tank water to wash it down the airline tubing. Dip water from the tank and pour it into the funnel cup, letting it force the sand down the tube.
Dry sand will NOT pour -- it has to get wet in the funnel cup before it will go down into the tank. I use sand out of the bag with no rinsing and have never had trouble. (If small amounts of lite twig-like organic matter float up to the top out of the new sand, just net them out and discard them.)
You want to keep the end of the tube right on the bottom of the tank so the sand doesn't fall free through the water column and cloud things up, but is deposited directly on the bottom. Just lay the sand into the trench you made. Ultimately you want your new sand bed several inches deep, but for now make it only as deep as you can pile it up without it spilling over into adjoining areas of CC too badly.
If all goes well, repeat this process each session until you have done the whole tank. Once all the CC is gone, work on deepening the DSB to full depth by regularly piling new sand in the front corners and letting the critters in the tank distribute it over time until the bed is up to depth. Lift live rock up a bit if the base gets buried too much. The idea is to add depth very gradually, giving any live critters time to move up and not get buried deeper than they like.
And that's it. Not much fuss and fun to boot.
