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I ended up just using the rsync command from my first post.
I didn’t expect it to work but, Everything seems to be back to normal now.
Although I didn’t know I could merely just reinstall the RetroPie manager.
Thanks @mitu!
@remino just make sure you keep updated backups.
@jplank
Have you tried an MicroSD card to USB adapter on your Ubuntu machine? The partitions should just mount normally.
