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If you care about the books, as you seem to do, then you have several good backups of them. If you do something very wrong and tell calibre to delete the books when importing them, then you can easily restore the books from your backups.
It is possible to import copies of the books into calibre and leave the original books where they are.
It is also possible to later add tags and other metadata to the books so that you then can save the books to the exact same folder structure you have now. Or one even better and more wonderful.
You can also use calibre to create a catalog over the books and "publish" your collection on your network. And do searches and conversions and update covers and metadata and even edit the books and much more.
In calibre the books will be stored exactly as calibre require them to be stored, and you can't do anything about that. But you can at any time save a copy of all the books to some other place as well. With a wonderfully intricate hierarchical folder structure that feels very meaningful to you.
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