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Do these bookmarks show up only when viewing the PDF from the Kobo or also from a desktop PDF reader? If they do not show up from a desktop reader, I suggest making a copy of the PDF in question, clear all the bookmarks from the copy using your desktop software, re-adding just one, and then copying it to your Kobo to see what it looks like.
On a side note, and I really hate to do this (sorry), but do I understand you correctly in that you can add bookmarks regularly to .PDFs from your Kobo? Or at least you used to be able to add bookmarks to PDFs from your Kobo? I ask because I use PDFs near exclusively on my Kobo (academic papers) and have never seen this functionality.
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