We use computational modeling to determine the mechanical response of crosslinked nanogels to an atomic force microscope (AFM) tip that is moved through the sample. We focus on two-dimensional systems where the nanogels are interconnected by both strong and labile bonds. To simulate this system, we modify the lattice spring model (LSM) to extend the applicability of this method to a broader range of elastic materials. Via this modified LSM, we model each nanogel as a deformable particle. We utilize the Bell model to describe the bonds between these nanogel particles, and subsequently, simulate the rupturing of bonds due to the force exerted by the moving indenter. The ruptured labile bonds can readily reform and thus can effectively mend the cavities formed by the moving AFM tip. We determine how the fraction of labile bonds, the nanogel stiffness, and the size and velocity of the moving tip affect the self-healing behavior of the material. We find that samples containing just 10% of labile bonds can heal to approximately 90% of their original, undeformed morphology. Our results provide guidelines for creating reconfigurable materials that can undergo self-repair and thereby withstand greater mechanical stress under everyday use.