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I hadn't realised either that when I open a PDF in Calibre it wasn't using a PDF reader. However,when I open the PDF that I've annotated in Goodreader I see everything except bookmarks, exactly as I made them. One thing I hadn't mentioned, and perhaps it has some bearing on itimpi's comments, the PDFs I'm working with are almost exclusively microfilmed books that I have download either from Google books or Archive Org.
Apropos surealmind's comment regarding Acrobat. I'd love to try it and having flattened the bank to buy the iPad my pockets are not quite deep enough at the moment!!
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