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I don't think so... that info is stored in the Aldiko database. CC merely stores the ebook files, and tells ereader apps to open the ebook. The ereader app then remembers the location of the book for the future.
tl;dr
If you want Aldiko to forget about a book, you must directly tell Aldiko to forget it.
Deleting the book from memory would probably cause the app to forget it too, since it cannot find it anymore.
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