Understanding the structural defects in GaN substrates as well as the formation and eradication of defects in Mg-implanted and annealed GaN provides a pathway to produce high-power vertical GaN diodes. Double crystal X-ray topography combines well with device performance to demonstrate how the improvements in substrate crystallinity correspond to improvements in device performance. Using high-quality substrate for ion implantation measurements helped clearly show that pyramidal inversion domain defects are observed to form upon annealing GaN at temperatures in the 1000–1300 °C range but were found to be dissolved or prevented from forming upon annealing at higher temperatures. Here, advanced characterization techniques—high-resolution X-ray scattering and electron microscopy—were employed to determine the behavior of these defects as well as to understand how the material recovers after the Mg implantation step. This study leveraged high-quality GaN homoepitaxial wafers as well as a novel high-temperature, high-pressure annealing technique that preserved the pristine GaN surface.