A seismic modeling system may include a seismic model data storage device, and a processor cooperating with the seismic model data storage device to determine a first 3D boundary around a suspect region within a first seismic model spatial domain data set for a geological formation at a first time, and determine a second 3D boundary around the suspect region within a second seismic model spatial domain data set for the geological formation at a second time and after movement of the suspect region. The processor may also compare the second 3D boundary to the first 3D boundary to determine an overlapping portion where the first and second 3D boundary regions overlap, and at least one non-overlapping portion where the first and second 3D boundaries do not overlap, and inpaint the overlapping portion based upon the at least one non-overlapping portion.