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I don't have library books so someone who does may have a better suggestion. However is there any need to keep books in the Reader Library folder after downloading, if your intent is to manage them via Calibre?
If not, then why not just delete them out of the Reader Library folder after adding to Calibre? Or does the Reader Library application complain if you remove files from its folder the next time you use it?
The only other alternative that comes to mind would be to sort the Reader Library folder by date, so your most recent downloads would hopefully be at the top. Copy those to an import folder, and delete from that import folder after adding to Calibre. That still leaves your books in Reader Library after you eventually delete from Calibre, but managing a Sony application's content is not exactly in Calibre's scope.
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