Ouch.
I had a similar issue on mine when I deleted a bunch of the .profle fies.
I found that when I opened the Adode desktop app and double clicked on the device bookshelf all of the books were listed but, marked as missing. I did a shift click to highlight the beginning and the end of the missing books list and I pressed the delete key to clear the list.
I don't know if that will help in this case.
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