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PDFs are designed on a fixed layout and the page numbers are part of the text of the page and therefore get rendered as such on eReaders. Sony's PDF reflow mode is helpful but cannot eliminate these hard-coded page numbers.
You could try converting to ePub which can allow you to strip out PDF page headers/footers, (which typically includes these page numbers). If the PDF is quite simple this can work well, but generally PDF to ePub conversions need some manually post-conversion editing to complete the job.
I haven't seen a justification option for the reflow mode but this is something else that could be achieved by conversion to ePub.
Last edited by Agama; 12-29-2012 at 10:07 AM.