It appears to me that the issue has something to do with the disk being listed as GPT vs MBR, which means the disk can't be marked as active. The only way I have found to fix this is to wipe the drive, which I don't want to do. That would make sense why taking an image of another one would "fix" it, but not sure how it got changed in the first place.
At a loss as to how to fix. I can take an image using HPDM, but that takes much longer and doesn't work well when in a remote location.