There is a manual for script commands to maintain in my administration, which is over 300 pages big, heavily linked (mainly into itself, but there are a few external links) and reasonably formatted. Whenever I need this word document converted to PDF, I use my portable version of LibreOffice.
LibreOffice can save directly into PDF, there is no need to install a PDF printer driver at least. The resulting PDF remains formatted and all links are fully functional (as in: they show up in the bookmarks functionality of PDF's!).
None of the (free) PDF printers I tried was able to manage this. Mind you, I don't use LibreOffice to edit this document, the only thing happening is loading the word document and saving it to PDF. In my (anecdotal) experience, the PDF generator from LibreOffice stands heads and shoulders above the rest.