There is a real risk here though, depending upon how long the tank has been the way it is. Areas of the substrate under chunks of wood or rock or other decor can become anaerobic. This is not a problem if it is left alone, as it provides the second part of a healthy substrate and aquarium water. But if disturbed or especially removed, the anaerobic patch in the substrate can kill fish fairly quickly. We had a member here a couple months back who killed all the fish in her tank doing this.
One way to avoid (hopefully) this while still leaving the fish in the tank is to have your water changer in hand, and as you move the wood do a very deep vacuum under every bit of substrate that was under the wood. You will probably see some pretty black water, depending upon how long this has been set up, and that is what could kill the fish if not removed.