The "Missing Project" problem has been solved; however, the Search and Index tabs for the Main Project do not work.
When you say the search and index don't work, do you mean that the results do not include topics in the merged projects? If so, you may want to look at the path to the merged project CHMs in the projectname.hhp file. Open it in Notepad and look for the [MERGEDFILES] section. In there you should find a reference to your CHM and more than likely there is a path prefix. Remove the path and recompile.
If I understood you correctly, you meant for me to go to the MainProject.hhp file ... so I did, and found no [MERGEDFILES] section; instead these are the sections in the .hhp file:
[OPTIONS] (several entries in this -- Compiled File, Title, Contents, etc.)
[FILES] (lists the files that are in this particular project)
[ALIAS] (no idea what this is)
[MAP] (...or this)
[TEXT POPUPS] (...or this)
Would it make any difference if I specified that I'm working with RoboHelp 6...?
I visited Peter Grainge's website and thought I found what I was looking for: in Reverse Engineering, there is a topic titled "Index and TOC Lost"
One of the directions says to "Locate toc.hhc and index.hhk and rename them as yourproject.hhc andyourproject.hhk."
I seem to be missing toc.hhc and index.hhk.
the mystery continues...