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That message is coming from aldiko.
When you tell CC that you want to read a book, CC will start the reader app you chose, in your case Aldiko, telling it that you (the user) want to "view" the book. CC has no control over what that reader app does when it starts. Apparently Aldiko is interpreting CC's request to view the book as meaning "put the book on the bookshelf." Further, it seems that Aldiko is refusing to do that work a second time.
Bottom line: Aldiko is confounding a request to view a book with a request to add a book to Aldiko's bookshelf. I see three workarounds, in order of what I think works best:
1) Use a different reader that doesn't insist on copying books from CC to its own library. There are lots of them. I have tried Moon+, FBReader, Cool Reader, and Mantano. I use Moon+.
2) Remove books from Aldiko's bookshelf when you are done reading them so that the next time CC asks Aldiko to view a book, it can add it to its bookshelf again. This has the advantage of removing the extra copy of the book that Aldiko makes.
3) Use Aldiko's bookshelf exclusively. In this case CC would act only as a transport to get books onto the device. This choice has many downsides, the biggest being that Aldiko does not see all calibre metadata and cannot update the metadata without resending and reimporting the book into Aldiko.
Perhaps someone else who uses Aldiko will have other suggestions.
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