The certified flight instructor and the student pilot were on an instructional flight to practice autorotations and simulated engine failures. About 45 minutes into the flight the instructor noticed the engine tachometer read lower than the rotor tachometer. The student pilot checked the battery voltage and said that it was "low". The instructor reported that the engine's fuel pump and ignition systems were not independent and he did not want to risk a downwind autorotation landing. When the instructor saw the rotor tachometer drop to 90 percent, he initiated an autorotation, assuming the helicopter had or was about to lose engine power. During the landing the left skid sank into the soft terrain and the helicopter subsequently rolled on to its side. The helicopter sustained substantial damage during the precautionary landing.