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This is a case of a bad message from CC. Assuming that the book is not an epub, it is indeed uploaded to calibre but only for metadata analysis. It is not automatically added to calibre's library because neither CC nor calibre know whether it is already there, perhaps with a different title or author.
You must resolve this question manually. In calibre's device view, find the new book, right click, then select either add book to library or match book to library.
I will change that CC message to (I hope) reduce the confusion.
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