A combination of electron microscopy and theoretical calculations provides new insights into the structure, electronics, and energetics of point defects and vacancy lines in BN single-wall nanotubes (SWNT). We show that the point defects forming under electron irradiation in the BN SWNTs are primarily divacancies. Due to the partially ionic character of the BN bonding, divacancies behave like an associated Schottky pair, with a dissociation energy of around 8 eV. Clustering of multiple vacancies is energetically favorable and leads to extended defects which locally change the nanotube diameter and chirality. Nevertheless these defects do not alter significantly the band gap energy, and all of them have electronic structure similar to that of BN divacancies. We thus conclude that under irradiation BN SWNT may have a very stable alteration of its electronic and optical properties.