Ion implantation into a-SiO2 leads to the self-assembly of nanocrystal arrays having application in optical and nonvolatile memory devices. It was recently noted that nanocrystal nucleation occurs in oxide regions exhibiting variations in oxygen concentration resulting from preferential sputtering. Here we report quantum-mechanical calculations that probe the atomic-scale dynamics following ion-induced low-energy recoils and show that preferential sputtering does not result directly from short-time collisional processes. These processes do, however, result in a population of loosely bound oxygen atoms connected to the amorphous network by a single Si-O bond. Thus, the well-known diffusion and relaxation processes that control stable defect formation at long times following recoil events lead to variations in O concentration in damaged regions.