If I understand correctly, the first principal axis has the smallest moment of inertia and the greatest kinetic energy. Anything that can dissipate the kinetic energy (like soil or water generating heat) will cause the ship to not be able to maintain that rotation and in order to conserve angular momentum it will instead rotate around the other stable axis—the third principal axis or end-over-end—since that axis has the greatest moment of inertia and minimum kinetic energy.