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I did the test mentioned yesterday. It was really successful. All the Annotations and Outlines (that had been added in Goodreader) appeared, completely unchanged and fully functioning after the document had been transferred into a Calibre library. In fact the only thing different to navigating around the document in Calibre, as opposed to in Goodreader, is that bookmarks are not available. That really isn't a great loss as most bookmarks I put in are temporary.
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