I really only use SoPDF for personal viewing, and then I don't find adding bookmarks to be worthwhile.
Since I'm a LaTeX user, if I wanted to do this, I do such things with pdflatex and the pdfpages and/or hyperref packages.
However, what is your input file format? Already PDF? Do the PDFs already have bookmarks, and you're just trying to preserve them through the conversion process, or are you adding new ones?
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