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(Abridged) We present a large sample of o-H$_2$D$^+$ observations in high-mass star-forming regions and discuss possible empirical correlations with relevant physical quantities to assess its role as a chronometer of star-forming regions through different evolutionary stages. APEX observations of the ground-state transition of o-H$_2$D$^+$ were analysed in a sample of massive clumps selected from ATLASGAL at different evolutionary stages. Column densities and beam-averaged abundances of o-H$_2$D$^+$ with respect to H$_2$, $X$(o-H$_2$D$^+$), were obtained by modelling the spectra under the assumption of local thermodynamic equilibrium. We detect 16 sources in o-H$_2$D$^+$ and find clear correlations between $X$(o-H$_2$D$^+$) and the clump bolometric luminosity and the dust temperature, while only a mild correlation is found with the CO-depletion factor. In addition, we see a clear correlation with the luminosity-to-mass ratio, which is known to trace the evolution of the star formation process. This would indicate that the deuterated forms of H$_3^+$ are more abundant in the early stages of the star formation process and that deuteration is influenced by the time evolution of the clumps. In this respect, our findings would suggest that the $X$(o-H$_2$D$^+$) abundance is mainly affected by the thermal changes rather than density changes in the gas. We have employed these findings together with observations of H$^{13}$CO$^+$, DCO$^+$, and C$^{17}$O to provide an estimate of the cosmic-ray ionisation rate in a sub-sample of eight clumps based on recent analytical work. Our study presents the largest sample of o-H$_2$D$^+$ in star-forming regions to date. The results confirm that the deuteration process is strongly affected by temperature and suggests that o-H$_2$D$^+$ can be considered a reliable chemical clock during the star formation processes, as proved by its strong temporal dependence., Comment: 18 pages, 8 figures and 6 tables. To appear in A&A