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Being able to reflow PDFs depends on how the PDF was made in the first place, which isn't something Kovid has any control over. Well-made PDFs convert fairly easily to other formats; other PDFs don't.
I believe the iRex series is the only set of devices that have good annotation features, although perhaps the Sony 600/900 has some. (Maybe it's just that the iRex devices are the only ones large enough to comfortably display most PDFs, and still have annotation ability.)
We're still a ways off on the ability to use ebook readers to comfortably mark up PDFs for professional & academic use.
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