Hmm... I don't know about a 90% water change. That could put your fish in shock. Before you decide to put them back in the tank make sure the temprature is at the adequate level and of course add chlor-away, or something similar that will de-toxicify the tank.
Also before adding the new rocks in the tank, take some distilled white vinegar, and put a few drops on the surface of the rock. If the vinegar begins to bubble, those rocks are not suitable for the tank. If nothing happens you are okay to drop them in.
On a final note, make sure to boil them (the rocks) in a pot of water to ensure they are sterile.
Good Luck!