Version of ID?
It would help a lot if you post sme screen shots of both the TOC dialog and the resulting bookmarks.
Are things correct the first time you make the TOC, and the mistakes happen only on update, or is it always an issue?
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Are things where they belong in the TOC? They don't appear to match the organization in the panel. It would help to also see the TOC setup dialog.
You should verify that each of the styles that is included in the TOC is assigned the correct level in the setup dialog.
Were these bookmarks generated by the TOC, or did you create them in the panel? My recollection is that the TOC does not generate bookmarks in the panel, but honestly I don't believe I ever looked as I don't need them inthe kind of work I do, which is for print. I have generated PDF bookmarks from a TOC, though, without a problem.
OK, thanks to your last message, I started to explore the Table of Contents dialogue box, and figured out what the problem was. It had to do with the levels I had assigned to the table of content items, which I had mismatched. Now I have the correct levels assigned to the right table of contents items and it updated the bookmarks perfectly!
Thanks for all your help.