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I respect the amount of work you've done.
However
Calibre doesn't care. When you import the books it will put them in it's own location (or the location you set) and then use it's own internal scheme for how things are organized.
Basically click on the little menu arrow next to "Add Books" and select the appropriate "Add books from directory and sub directory" option and let it run.
In the future as you download new ebooks just put them in a download directory and tell Calibre to import them and let Calibre do all the "heavy lifting".
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