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If you add the books to calibre your old folders and archives become redundant. No need to keep them, except for backup.
Calibre can treat folders with ebooks either as containing different books or the same book in different formats.
I would recommend you to experiment with calibre. Pick a few books, perhaps twenty, and try to create the perfect calibre library with them. Perfect metadata and covers. Custom columns. Save templates. And so on. It takes a while before you understand how very different calibre is from managing ebooks in folders.
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