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In order for optical cavities to enable strong light-matter interactions for quantum metrology, networking, and scalability in quantum computing systems, their mirrors must have minimal losses. However, high-finesse dielectric cavity mirrors can degrade in ultra-high vacuum (UHV), increasing the challenges of upgrading to cavity-coupled quantum systems. We observe the optical degradation of high-finesse dielectric optical cavity mirrors after high-temperature UHV bake in the form of a substantial increase in surface roughness. We provide an explanation of the degradation through atomic force microscopy (AFM), X-ray fluorescence (XRF), selective wet etching, and optical measurements. We find the degradation is explained by oxygen reduction in Ta$_2$O$_5$ followed by growth of tantalum sub-oxide defects with height to width aspect ratios near ten. We discuss the dependence of mirror loss on surface roughness and finally give recommendations to avoid degradation to allow for quick adoption of cavity-coupled systems.