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Originally Posted by compurandom
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.
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I assume by "category" you mean "collection". If so, the only way a book can be in a collection is if it is in the database. And, it will also be displayed in the main library list. If the book is missing elsewhere in the database, it's possible the collections list will show the wrong count of books in a collection, but even that I would be surprised at.
This probably comes down to me not knowing what you mean by "ghost books". I took a guess, but that doesn't match with what you seem to be seeing.
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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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When I talk about a corrupt database for the Kobo device database, I nearly always mean invalid tables, pages, indexes etc. Things that are found doing the database check. Not inconsistencies between the tables. I don't check this very often, but I rarely find any problems with it. I would be curious to see the database you had after the restore to see what happened. But, it's probably to late now to see what was happening.