I once jerry-rigged a project by linking a book to the start file of a child project within the merged project folder. That way only the child project launched when you clicked the link. However, since that project was also merged, the child topics also displayed in that folder. It was the only way I could think of to have it both ways, with merged and un-merged projects all in one. This was back in RH6 days. They may have come up with a way to isolate searches and indexes since, but I haven't needed to look for it.
If not, and you're just trying to narrow the search, this might work for you. However, the child index is still going to merge with the parent in the larger project.