Sorry, my mistake; it's not on the "Advanced" menu, it's on the top-level library menu itself, immediately under the 5, 10, 20 items per page options.
From what you've said, she does NOT have folder view enabled. If folder view isn't enabled, you only see the books that are in the "ebooks" folder (and its sub-folders), so anything outside that folder wouldn't show up. By moving the books into the "ebooks" folder, they are now showing up. They'll show double if the same book is in two different folders.
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