I think it really has to do with how long the tank has been set up. 5 years and you are most likely bursting a bunch of sulfur pockets. On the other hand, I have replaced 80% of my substrate in dozens of different tanks and never had a single problem. It usually kicks up a bunch of brown debris and blah blah blah........
My advice would be to follow the above advice as precautions though, LOL, unless your tank is fairly old. Also, if you are doing this after a few months - then I would probably have an extra canister filter on hand with a WICKED huge amount of carbon on hand. Sometimes, it can be more stressfull to move the fish then to move your live rock. If you go chasing them around the tank then burn their little gills by letting them touch air, etc. I find it best to move the stuff around with a full tank. That way there is more surface area for the detritus to float around in and more area for you to pump out. Have the above bucket of pre-mixed water available, and replace the removed water. Then usually just chuck on the canister filter and let it run for a bit.
What is the size and age of this tank? Those two are VERY important.