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Likely a common misunderstanding.
The first time you create printed documentation, the topics are based on the TOC. Thereafter there is no link.
When you add new topics to the project, they are not automatically in any of the TOCs. You have to add them to each TOC. It's the same with print, you have to add them in the print layout.
Easiest way is to simply use the double left chevrons to remove the topics in the print layout and then use the double right chevron to back in, the difference being it will add all the topics in the TOC and as you added the new topics there, they will be in the print layout.
There's more in Printed Documentation on my site.
See www.grainge.org for RoboHelp and Authoring tips
Yes, as I suspected it was an easy fix. I just created a new printed documentation layout, and it generated fine. I assumed regenerating the original one would update the TOC and content, but it seems not.