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Laser machining is frequently utilized in the manufacture of photovoltaics. A natural by-product of these fabrication processes, heat, not only serves as a means of material removal but also modifies the material in an extended region beyond that ideally intended for alteration. This modified region, termed the heat affected zone, is detrimental to performance and should therefore be minimized. While undoubtedly thermal in origin, it is unclear exactly how the thermal environment during laser machining correlates to changes in the PN-junction that reduce performance. In response, we combine in-situ Raman based thermometry measurements with post-event failure analysis to identify the physical mechanisms damaging the junction during laser machining. From this approach, damage is shown to initiate prior to melting and be driven primarily by the diffusion of dopants for fluences that do not induce ablation. Additionally, comparatively small regions of damage are shown to have a large impact on operation.