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We report radio-frequency measurements of quality factors and temperature mapping of a nitrogen doped Nb superconducting RF cavity. Cavity cutouts of hot and cold spots were studied with low temperature scanning tunneling microscopy and spectroscopy, X-ray photoelectron spectroscopy and secondary electron microscopy. Temperature mapping revealed a substantial reduction of the residual resistance upon cooling the cavity with a greater temperature gradient and hysteretic losses at the quench location, pointing to trapped vortices as the dominant source of residual surface resistance. Analysis of the tunneling spectra in the framework of a proximity effect theory shows that hot spots have a reduced pair potential and a wider distribution of the contact resistance between the Nb and the top Nb oxide. Alone, these degraded superconducting properties account for a much weaker excess dissipation as compared with the vortex contribution. Based on the correlation between the quasiparticle density of states and temperature mapping, we suggest that degraded superconducting properties may facilitate vortex nucleation or settling of trapped flux during cooling the cavity through the critical temperature.