PDF is simply not intended for the purpose you describe.
PDF was designed to create a file that represents how a document would look with each element on the page (text, images etc.) being at a fixed point which represents the equivalent fixed point on a piece of paper (e.g. A4).
It is also intended to be an "archive" format, where the PDF is created and then no further editing or converting takes place.
PDF's structure as a file format represents this and as such it is hard for third party tools to attempt to convert a PDF to another format.
I think that the main problem with the Contents/Bookmarks in PDF is that they simply refer to a page in the PDF.
Once you convert a PDF to a .mobi or .epub file then you lose the ability to link to those pages.
Last edited by Daveoc64; 10-14-2011 at 10:02 AM.
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