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If you keep the default author directories, finding duplicates is going to be a real pain in the ass. I suggest you change the author directories to a single directory such as books.
You can then copy all of your eBooks in author directories to the new books directory. It's easy to do. In Windows Explorer, go to the root of your Kobo drive. Search for name: *.epub. When it's done, select all of the ePub files and cut and then past into books. Then select all of the author directories and delete them.
Then go into calibre and change the author directories to the single books directory.
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