When you use topics without TOC entries in combination with additional TOCs you may need to take additional action to ensure that the topic file is included in your output. An additional TOC acts like an include option for every topic it includes, and by default all other topics can be excluded. Because of this, topic files that are only accessed by hyperlinks and not by TOC entries may get excluded if you are not careful.
Method 1: Use the compiler option to force inclusion
This is the simplest solution. It tells Help+Manual to automatically include any topic file that is referenced with a link in your project. Just go to View > Program Options > Compilers and set the Handling of dead links option to Silently include linked topic. This will include all topic files referenced with hyperlinks, even if they don't have TOC entries. The included topic files will be listed in the compiler report.
Side-effect: This will also include topics that were excluded from the TOC with build options, if there are links to those topics that you have overlooked. Check the compiler report!