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I'm not sure if the ghost books remain in the database as books, but they certainly stay in the categories they were in. The only way I've found to clear them is to delete the category from the device, and then get calibre to re-add the rest of the books back to the category.
This time, there were only a few deleted books that were in the database backup, so I may have gotten them all already, but I've seen this before with database corruption and they never go away automatically.
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