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The "No" in the TOC column simply means that the bookmark has not been added to the TOC. This does not mean that the topic that contains the bookmark does not exist in the TOC as you can add both topics and bookmarks. If you add a bookmark to a topic and then add the topic to the TOC you will get the nehaviour you see. It is perfectly normal. Using bookmarks in the TOC can be way of fooling the user into thinking there are numerous topics in the TOC and when they click on a TOC page they are taken to the bookmark in the desired topic. Personally I don't use them as I find them rather disconcerting.
If you delete them, and you still have a link to them, the link will not work. If they are not referenced you can leave them there without it affecting your help file. If you go into your Link View tab you should be able to see if they are referenced anywhere or not.
Can I see if the bookmark is referenced, or just the topic? The infprmation on that link view doesn't seem that specific, or maybe I'm just looking at it wrong.
But it sounds like you are saying that it doesn't hurt anything to have alot of unused bookmarks - right?
btw - what does a yellow link line in Link View mean?
Yellow lines indicate that the link is from an image map. If the bookmark is mapped, the link view should show something like "topic1#bookmark1". The bookmark is referenced by the # character. If you can see this, the other end of the yellow line indicates the topic that contains the image map that has the link to the bookmark.
Unused bookmarks cause absolutely no problems at all. It's a bit like the spare tire in your car boot. If you delete a bookmark that is linked and save your project, you'll see a Broken Link in your Project tab.