We analyse the influence of optically generated non-equilibrium phonons on the spin relaxation and effective spin temperature of an individual Cr atom inserted in a quantum dot. Using a three pulses pump-probe technique, we show that the spin relaxation measured in resonant optical pumping experiments strongly depends on the optical excitation conditions. We observe for an isolated Cr in the dark a heating time shorter than a few hundreds $ns$ after an initial high power non-resonant excitation pulse. A cooling time larger than a few tens of $\mu s$, independent on the excitation, is obtained in the same experimental conditions. We show that a tunable spin-lattice coupling dependent on the density of non-equilibrium phonons can explain the observed dynamics. Low energy excitation conditions are found where the Cr spin states S$_z$=$\pm$1 can be efficiently populated by a non-resonant optical excitation, prepared and read-out by resonant optical pumping and conserved in the dark during a few $\mu$s.
