We investigated the surface morphology changes in a 2 inch-diameter, c-plane, free-standing GaN wafer using X-ray diffraction topography in a grazing-incidence geometry. We observed a decrease in the peak intensity and increase in the full width at half maximum of the GaN 114 Bragg peak after the deposition of a homoepitaxial layer on the same GaN wafer. However, the lattice plane bending angles did not change after homoepitaxial layer deposition. Distorted-wave Born approximation calculations near the total external reflection condition revealed a decrease in the X-ray incidence angle of the 114 Bragg peak after the homoepitaxial layer deposition. The decrease in both X-ray penetration and incidence angle induced broader and weaker diffraction peaks from the surface instead of the bulk GaN.