You just have to be careful with moving the bottom peices because you can stir up one heck of a storm of detrius. I would shut the flow off in the tank, remove about 25% of the water into buckets, stick your rock and corals into those buckets, then do a little sucking to get rid of the nasty stuff that has been undoubtly disturbed and then re-reefscape.
Fill with new saltwater and it might not hurt to dose some sort of stablility chemical to help get your parameters in check faster. Also make sure to do water testing to make sure nothing creeps up on you and bites you
Asuming you have hardy fish they should survive, but if you can get them out it will be better for them.