While the skeletons were wearing armor made from the crystal, it didn't protect them from the heat, for they merely had a VERY high melting point. Bone...Not so much. As they wore the armor, they were cooked by the rock, being scorched black, and reduced to ashes by the heat.
The shadow energy ball itself was met by a torrent of fire, which acted as a wall, incinerating the magic itself for fuel for its own blazes, thus dissipating the energy ball itself. The flames then went for Pedalos, these the flames of the continent itself. Blazes which could use magic itself as fuel...