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Instead of the library program you can also drag and drop the book-files directly in windows explorer (or finder on Mac). It doesn't matter in which location you drop the files. The reader will check all available memory (Memory card slots and internal reader memory) for books and then show them according to their file properties (not the file names).
Once you have the files on the reader, you can open the library program again and sort your books on the reader into collections. No sync necessary. Once a book is dragged to a collection and you disconnect the reader, the book will show up in the collection.
You can also check out calibre as a replacement for the Sony program. I cannot give you more on that though as I prefer arranging my files in folders. And any Database will sort and store the files according to its internal settings. So this way you could also end up with the same book in different folder locations if you use any of the databases.
Maybe this helps a little.
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