You could continue to use either of these solutions, probably the alternate TOC would be my preferred one, but you'd also need to manually amend the master project's HHP file. It has a [MERGED FILES] section that will include the CHM you do not want. If you remive that line and recompile the master you should find the child CHM is excluded.
Just popping in to say that you may find it simpler to just rename the .HHP and let RoboHelp create it for you again when you generate the project.
Additionally, I have a nagging lingering memory that there was a rather generic issue with merged CHMs where you shouldn't have a merge appearing as the last entry in the TOC. Perhaps consider adding a page that you link to at the very end of the TOC.
Helpful and Handy Links
Thanks for the ideas. Regrettably,..
* if I delete the HHP file, then RoboHelp generates it with all merge references again
* if I manually remove a subproject from the Merged Files section, then the topics of that CHM cannot be found over the search in the full output as well, i.e., the topics appear in the TOC but not in the search.
I found now though that a combination of conditional build tags (to remove the unwanted subprojects from the TOC) and then manually deleting the not needed sub-CHMs in the output folder appears to do the job. Having a single setting to adjust for good would have been more convenient, but this is acceptable too.