WebHelp output is generated (to your local machine) and published (usually to a server), not compiled. The output for each "child" project must obviously be targeted to its own correct folder.
The Generate target directory is on the first page (General) of the wizard and the Publish target directory is on the fourth page (Publish). Verify both targets, since either or both are obviously incorrect.
I seem to remember someone also having problems where the Publish (server) location refused to update. I can't remember what the solution was for that - either deleting a file, or publishing to a different location I think. Maybe someone else can remember more details?
My understanding is that the output of merged projects is placed into Webhelp\Compile\Webhelp\mergedProjects
By default the generated output will go to the SSL folder for the project. You can copy that to the relevant folder under mergedProjects but it would be more efficient to change the output folder so that it generates to the relevant child folder under the mergedProjects folder created when the parent is generated. You will need to change this in the first page of the wizard and do that for each child project.
What is puzzling is that unless you did that when you first generated, how did you get it to work then?
See the Merged Projects topics on my site.
See www.grainge.org for RoboHelp and Authoring tips