If my memory of this is still intact, I believe that in order for the Indexes to properly merge, you need to ensure that all of them are configured as Binary indexes. To check this, open each project and press Ctrl+Shift+Question Mark to display the Project Settings. From the General tab (1) enable the Binary Index check box (2).
Click OK and recompile all the component CHM files.
I have checked all projects and they are all marked that way. The merge has been working for years but stopped showing the combined index a few weeks ago. I haven't had time to investigate why until now.