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An easy method for separating out which books are not in the database but are physically listed in the file structure is to use the Library=>Switch/Create Library=>Move the current library to a newly specified location option.
This will create a new library and move all of the books currently listed in your database to a new location. The books remaining in the old location are the ones that were not listed in the database. You can then work on adding them back into your library and, as long as you do not have Automerge selected in the Preferences=>Add Books section, it will notify you if you are trying to add any duplicates.
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