We went BB in our three reefs when we upgraded all three tanks almost two years ago. That meant we removed all the livestock from the existing tank, got rid of the sandbed so we could put the new tank/stand in place of the old tank/stand. Had lots of NSW on hand, but used quite a bit of the old water to fill the new tank. Rock from the old tank was swished in old tank water to remove detritus, and there was LOTS of it.
The sandbeds in each of the three tanks was 2-3" deep. Once everything was out of the tank, I stirred the sandbed really well with the remaining 2-3" of tank water. There was a raunchy rotten egg stench to the water after stirring. These were not what I would consider deep sand beds in the least, yet at least some of the bed had gone anoxic and had released hydrogen sulfide.
Because of the possibility of releasing hydrogen sulfide into your water column, I would suggest you take the time to be safe with your livestock if you go BB and tear down your tank to remove the sandbed. That way, you can get a very clean start, have new aquascaping, and be sure you won't have an unintended disaster on your hands.
Here's a new addition to the Reef Chemistry page on
Hydrogen Sulfide and the Reef Aquarium:
http://reefkeeping.com/issues/2005-12/rhf/index.php
Personally, I won't go back to using sandbeds EVER!