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Please look into getting Calibre for solving this type of problem. It shows you what is on your device and would let you add those to your Calibre library. Then you can use the same interface to delete them from your device. As you library builds up, it would get more and more difficult to manage the library in file system or only on your device (as you have already noticed). Calibre solves this problem by allowing you to tag, search and manage your books a variety of ways. No affiliations. Just a satisfied user.
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