Join Date: Dec 2009
Location: Philadelphia, Pa
I've definitely stirred up some pretty serious flourite clouds during re-scapes and never lost a fish, but you would definitely want to take them out for a complete redo. First to avoid any accidental trauma while your digging around in there. Second, you're pretty like to have the tank re-cycle if you take out all of the substrate (that's where a large part of your beneficial bacteria live) and replace with new, uncycled substrate. So, you should take the fish out and keep them out until you can make sure your ammonia/nitrite levels won't spike.
Out of curiosity, why are you bothering to swap? I've not used floramax, but from what I can tell, flourite and floramax are pretty similar.