The skeleton shattered after losing his existence. The dust that came out of his already destroyed body flew toward Noah and helped fix his injuries.
The effects were barely noticeable, especially as Noah deactivated his empowerments. The unstable substance, Isaac's ability, and ambition left him with a deep sense of weakness that slowed down his requirements and forced the black hole to invest more energy in dispersing stress. Still, he didn't face any deepening of his injuries, and his body remained stable.
Those drawbacks appeared unable to affect Noah deeply. His body was advancing slowly, but each step taken forward consisted in a massive increase in power. The same went for the black hole due to its connection with his dantian. The latter's improvements would multiply after reaching the fourth center of power.