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Were the hyperlinks created through the Hyperlinks panel or with the Buttons and Forms Panel? If they are done as real hyperlinks then the pdf can be output as a Print pdf (make sure that Hyperlinks is checked in the Export Adobe PDF dialog window—see screen shot) rather than an Interactive PDF. I have had much better luck with the navigation remaining intact with this type of a pdf.
Just attempted this and the export still isn't working correctly. The links will land in-between two pages rather on the start of the page it is supposed to be linked to, but it works fine before the upload, so it is whatever is happening in the upload process that messes with it.
Thank you for your help though!
Happy to help.
bahchangeup wrote… Further more, when I export this as an interactive PDF and upload it to the web the hyperlinks are messed up and do not go to the correct spot within the document when clicked.…
Will it work when the PDF is opened in the desktop version of Adobe Reader on Mac OS X or Windows?
If you open a PDF in a web browser this will be a totally different thing. Depending on the browser's version or even the device a PDF reader in the browser could fail.
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Did you make the hyperlinks to go to a specific hyperlink destination anchor? Or to just the "page" in general?
Hyperlinking to a specific destination text anchor has worked very well for the past few editions of InDesign/Acrobat. Our studio hasn't seen any problems with this is several years.
But hyperlinking to the page has been a bit weird at times. In our studio, we haven't yet been able to confirm what causes this but we suspect that it might be "paging" to the first item in the PDF's architectural/construction reading order on that page, which correlates to the bottom-most item in InDesign's layers panel for that page.
FYI: Stacking order in InDesign's layers panel produces the architectural/construction order in the PDF.