work, we specifically investigate the process of argon milling, a potentially coherence limiting step, using niobium and aluminum superconducting resonators as a proxy for surface-limited behavior of qubits. We find that niobium microwave resonators exhibit an order of magnitude decrease in quality-factors after surface argon milling, while aluminum resonators are resilient to the same process. Extensive analysis of the niobium surface shows no change in the suboxide composition due to argon milling, while two-tone spectroscopy measurements reveal an increase in two-level system electrical dipole moments, indicating a structurally altered niobium oxide hosting larger two-level system defects. However, a short dry etch can fully recover the argon milling induced losses on niobium, offering a potential route towards state-of-the-art overlap Josephson junction qubits with niobium circuitry.