Best way I could think of is to create a folder on your PC called Xbox. Inside this folder create different folders for each drive letter you see when you ftp to the xbox. Then use ftp to transfer the contents of those folders to the folders you created on the pc.I think I've found something relevant in an old post on another forum (not sure if I can link it?):
Which made me realize the PS2 core was the one I had trouble with. I transferred some files and games in an attempt to make it work, then deleted them, and that's probably when the problems started.
At some point I also tried to restore Retroarch's config with the apposite option and it crashed, which I thought was weird.
Then I thought a full factory reset would fix the issue by wiping/rebuilding the SSD but... apparently not?
Now I'm trying to find what the entire file structure should look like out of the box so I can compare it to mine, but no luck so far
Everything should be as it is out of the box if you did a factory reset. If you have a friend with a series s and they are willing to let you open their console you could clone their working drive to yours. When you put the newly cloned drive into your xbox, do a factory reset and it should be as if nothing ever happened.