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CC's Cloud Connection can see books in honest-to-goodness calibre libraries stored in the cloud. CC cannot see books saved-to-disk or sent-to-folder. CC's Cloud Connection can see books only if they appear in calibre's Library View, not calibre's Device View.
My guess, given what you said, is that you stored books in a directory (folder) using Save to disk/Send to folder, where the destination folder is an empty calibre library. Doing the Save/Send does not add books to that library, but instead actually corrupts the library. You would see the corruption if you opened that library in calibre then used calibre's Check Library function. If you want to put books in an empty library so that CC will see them then you should use calibre's Copy to Library function, usually available by right-clicking on a book and choosing Copy to library. This function copies the book and adds that book to the calibre library database in the new library.
I need to ask: if you are using Send to folder then why not use CC's wireless device connection and send directly to CC?
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