While selecting nodes from the table of contents, below the TOC is a series of properties that are changeable for the selected node, and among those properties are the ability to selectively NOT output certain sections of your help file to certain output types under the "Export To" section of the Properties window.  For example, if you have several pages that are ONLY connected to context-sensitive help for your application, and should not show up in the PDF output for instance, then this takes two clicks: 1)  select the TOC node in question, and 2) click the PDF "button".  It changes appearance indicating that node will not be output to that type of output.