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The Sony software works ok for me, and I prefer it to ADE. All my books whether from the library or other stores like Kobo get loaded with my Sony purchases and stored neatly in the same folder. It's fine to delete a book from the Sony software if the book is stored in the Sony books folder for example. However, I think I remember a past post that you are loading your books into calibre and then importing them back into the Sony software. In that case you are creating pointers to these other locations. Sounds like your workflow is creating the complexity of what you see.
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