The substitution of hydrogen by deuterium is generally known to increase the stability of the defect passivation in semiconductors, occasionally giving rise to giant isotope effects.In this work, the stability under an electron beam irradiation of boron-hydrogen and boron-deuterium pairs in diamond are compared. The dissociation kinetics was followed in situ by cathodoluminescence spectroscopy. Surprinsingly, B-H complexes are more stable than B-D complexes under electron beam at low temperature (~ 100K), with a dissociation rate about twice smaller. These experimental results are coherent with a dissociation mechanism involving a cumulative vibrational excitation of the complexes.