Books not being imported is usually because there are errors in the books. When the device first sees the books, it extracts the metadata and ToC. If this fails, the book is not imported and can block further imports. You need to work out which books have not been imported and have a look at them to work out the issues. If they are epubs, running a conversion in calibre will usually fix any problems. Or fail which means the book had big issues. You can also open them in the calibre editor and use the error checking to see the errors.
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