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I know my previous message sounded pretty complex, but it is something that you would only have to do once. Thereafter calibre should be able to manage things fine for you.
As far as adding the books from your "Complete Library" into calibre after creating a new library... you would be able to do that by choosing the Add Books from Folders and Subfolders option of the Add toolbar icon (under the more button "v"). It should be able to walk your existing library structure and copy everything into the new library. However, with a lot of books, this could take some time to process.
PS: Sorry to hear about your cat.
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