Optomechanical resonators were fabricated on a silicon-on-insulator substrate that had been implanted with phosphorus donors. The resonators' mechanical and optical properties were then measured (at 6 K and room temperature) before and after the substrate was annealed. All measured resonators survived the annealing and their mechanical linewidths decreased while their optical and mechanical frequencies increased. This is consistent with crystal lattice damage from the ion implantation causing the optical and mechanical properties to degrade and then subsequently being repaired by the annealing. We explain these effects qualitatively with changes in the silicon crystal lattice structure. We also report on some unexplained features in the pre-anneal samples. In addition, we report partial fabrication of optomechanical resonators with neon ion milling.