When you use popup topics in secondary TOCs the popup topic files your links refer to will not be included automatically as they are when you use the primary TOC. The All Builds include option assigned to all topics by default only works automatically in the primary TOC.
When you are using multiple TOCs in your project and publishing a secondary TOC, any popup topics you link to must be included explicitly. You can do this in two different ways:
Option 1: Dead links handling options
Go to View > Program Options > Compilers and set the dead links handling option to Silently include linked topic. This is the simplest solution but it will also automatically include any excluded topic files that you may have referenced with regular topic links. So you should always check your compiler report for topics like these that you may have not wanted to include. You can then handle the links with conditional text to exclude them automatically.
Option 2: Set the build options of your popup topic files
Alternatively you can set the build options of your popup topic files to the output formats that support popups, which are WebHelp, CHM, eWriter, and Visual Studio Help (if you are using that). The eWriter format will be included automatically if you set WebHelp, so generally you will only need to set CHM and WebHelp.
1.Right-click on the popup topic file in Project Files > Topic Files and select Include in Builds in the context menu.
2.Set the include options to WebHelp, CHM and (if necessary) also VSHelp.