We study the effect of strain on the physical properties of the nitrogen antisite-vacancy pair in hexagonal boron nitride ($h$-BN), a color center that may be employed as a quantum bit in a two-dimensional material. With group theory and ab-initio analysis we show that strong electron-phonon coupling plays a key role in the optical activation of this color center. We find a giant shift on the zero-phonon-line (ZPL) emission of the nitrogen antisite-vacancy pair defect upon applying strain that is typical of $h$-BN samples. Our results provide a plausible explanation for the experimental observation of quantum emitters with similar optical properties but widely scattered ZPL wavelengths and the experimentally observed dependence of the ZPL on the strain.