After a number of resets, signing out of my account, syncing with the desktop app, I can always get to this point;
All the books are gone (I side load all my books through Calibre) and I have no shelves on the device.
I did lie earlier, I forgot that I do use the standard kobo plugin to create shelves. My apologies for the misinformation.
So anyway here is where I am, an empty device with no books and no shelves. When I reload my library with Calibre, double shelves again. But not all of them. In the pic I attached you can see the first shelf isn't doubled.
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