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Chaley has given you sound advice to save using your import/export procedure. However, adding the formats together does not equal total books, as books may have more than 1 format. The total seems to be the number of book records in the database. Sounds like your database is corrupt or there is something amiss with your configuration. Book entries with no ebook files can exist and I suppose are useful if you want to use Calibre to catalogue, say, a library of physical books. However, so far as I am aware you would need to actually import these records or tell Calibre to create them. Someone more knowledgeable about Calibre than I may be able to cast more light on the matter.
I am curious what files actually exist in the 3,000 records you are talking about. Presumably no files are snown on the interface. What files are in the actual directories?
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