Welcome to our community, Steven
Sorry for slowness, forums seem hit or miss today.
What you are describing is exactly how a merge should operate. All projects that are part of the merge should be properly searched and an Index would work across all projects. Because of this, I'm struggling to see a need to index everything from only the Master.
As you likely already know, the Smart Index Wizard simply scans topics and auto-maps them to keywords in whatever project you have open.
Sorry, but there is no way I'm aware of for the Smart Index Wizard to be used from the Master and coax it to index child projects. It's an interesting thing to consider and I would heartily encourage you to submit a Wish Form to ask for this functionality to appear in a future release. You do this using the Wish Form. (link to the Wish Form is in my sig)
Helpful and Handy Links
Thank you for your help. What I need is that when a user opens the help chm file produced by the master project, there is an index of all the projects. It sounds like you are saying that if I produce an index in each of the child projects, the user is have access to the complete index when opening the chm file produced by the master project. I will try to create the index in this manner. Do you have any idea how I can make the search work across all projects when the user opens the chm file from the master project?
Thank you again Captiv8r