We have investigated the oxidation/reduction behavior of dome-shaped three-dimensional islands of Ge on Si(001) grown by ultrahigh vacuum chemical vapor deposition. The oxidation was done by exposing the surfaces to H2O steam in N2. The reduction was done by H2, which selectively reduces only the GeO2. The results of the oxidation/reduction processes under varying conditions were analyzed by high-resolution transmission electron microscopy. We found that the selective reduction of such structures does not result in a perfect recovery of the former Ge dots, but results in phase-segregated Ge enrichments. In many cases these enrichments show epitaxial relationship with the underlying Si substrate. These structures are of potential interest for Ge dots embedded in an insulating material as well as for lateral epitaxial overgrowth of SiO2/Si(001) by Ge, using the reduced Ge dots as the seeds for epitaxy.