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I ran media cleaner and it found a lot of unused image files. I opted to have Media cleaner put them in the trash can. However, Shortpixel bulk optimizer somehow thinks those images still exist and try to optimize them. This results in a long list of “too many inaccessible URLs from same domain, please check accessibility and try again.”
I had two options: Restore all the images (which I did), or I guess permanently delete them. After the restore Shortpixel bulk processing ran flawlessly.