Boron bulk crystals are marked by exceptional structural complexity and unusual related physical phenomena. Recent reports of hydrogenated $alpha$-tetragonal and a new $delta$-orthorhombic boron B$_{52}$ phase have raised many fundamental questions. Using density functional theory calculations it is shown that hydrogenated $alpha$-tetragonal boron has at least two stable stoichiometric compositions, B$_{51}$H$_{7}$ and B$_{51}$H$_{3}$. Thermodynamic modeling was used to qualitatively reproduce the two-step phase transition reported by Ekimov et al. [J. Mater. Res. 31, 2773 (2016)] upon annealing, which corresponds to successive transitions from B$_{51}$H$_{7}$ to B$_{51}$H$_{3}$ to pure B$_{52}$. The so obtained $delta$-orthorhombic boron is an ordered, low-temperature phase and $alpha$-tetragonal boron is a disordered, high-temperature phase of B$_{52}$. The two phases are connected by an order-disorder transition, that is associated with the migration of interstitial boron atoms. Atom migration is usually suppressed in strongly bound, covalent crystals. It is shown that the migration of boron atoms is likely to be assisted by the migration of hydrogen atoms upon annealing. These results are in excellent agreement with the above mentioned experiment and they represent an important step forward for the understanding of boron and hydrogenated boron crystals. They further open a new avenue to control or remove the intrinsic defects of covalently bound crystals by utilizing volatile, foreign atoms.
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