When we went BB in our three tanks, we upgraded tanks at the same time, so we removed everything from the old tanks, got rid of the old tanks, then set up the new ones. Corals, fish and inverts all made it without incident in all three tanks.
Removing the sandbed was horrible
It reeked to high heaven
Anyway, I would remove everything from the tank to be safe. Once you start messing with the sandbed, you don't know how much toxic gas will be released. Also, removing everything will make sure your rock structure and corals don't topple which you'd end up having to rebuild.
Have a bucket of tankwater handy to swish each rock as it comes out. You'll be surprised how much detritus you'll get out of the rock
Dump the bucket when it gets too dirty.
Dedicate a day for the job, so you can reaquascape the tank at your leisure to get rockwork that you really like. And make sure you have lots of extra NSW on hand to make up for the water you use during the cleaning, storage and moving process.
Here's my page on maintaining a BB tank:
http://www.lostmymarblz.com/reeftips...ottomtanks.htm