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Despite several first principles studies, the relative stability of BN polymorphs remains controversial. The stable polymorph varies between the cubic (c-BN) and hexagonal (h-BN) depending on the van der Waals (vdW) dispersion approximation used. These studies are unable to explain the main experimental results, c-BN is stable, the relative stability order and the large energy difference between h-BN and c-BN (greater than 150 meV/formula unit). In this study, we introduce contributions from electron-phonon interactions (EPI) to the total energy of BN polymorphs. This clearly establishes c-BN is the stable polymorph irrespective of the vdW approximation. Only by including EPI contributions do the ab initio results match, for the first time, the main experimental results mentioned above. The EPI contribution to the total energy is strongly sensitive to chemical bonding (approximately twice in $sp^2$-bonded layered over $sp^3$-bonded polymorphs) and to crystal structure. The crucial role of EPI contributions is seen in $sp^2$-bonded layered BN polymorphs where it is greater than the vdW contribution. Given that h-BN is a prototype layered material, in bulk or 2D form, our results have a broader relevance, that is, including EPI correction, along with vdW approximation, is vital for the study of energetics in layered materials.