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The recent progress in the growth of large-area boron nitride epilayers opens up new possibilities for future applications. However, it remains largely unclear how weakly attached two-dimensional BN layers interact with their substrate and how their properties are influenced by defects. In this work, we investigate hBN layers grown by Metal Organic Vapor Phase Epitaxy (MOVPE) using Fourier-transform Infrared (FTIR) spectroscopy in the temperature range of 160-540 K. Our measurements reveal strong differences in the character of layer-substrate interaction for as-grown and delaminated epitaxial layers. A much weaker interaction of as-grown layers is explained by wrinkles formation that reduces strain at the layer-substrate interface, which for layers transferred to other substrates occurs only in a limited temperature range. The most striking result is the observation of a giant increase in the $E_{1u}$ phonon energy of up to $\sim6$ cm$^{-1}$ in a narrow temperature range. We show that the amplitude and temperature range of the anomaly is strongly modified by UV light illumination. The observed giant effect is explained in terms of strain generation resulting from charge redistribution between shallow traps and different defects, which can be interpreted as a result of strong electron-phonon coupling in hBN. The observed narrow temperature range of the anomaly indicates that the effect may be further enhanced for example by electrostrictive effects, expected for sp$^2$ boron nitride.