After several days of hair-pulling and a multitude of profanities, I finally fixed my problems. However, I did take an unexpected step backwards that I thought maybe worth a warning.
Completely uninstalling RoboHelp, purging the Registry and then reinstalling RoboHelp cured the disappearing folders problem but not the multi-windows to display merged help.
To cure that required removing the links in my TOC, copying all the child CHMs to the root of the parent project and then remerging the CHMs. When I regenerated the parent help, everything works great - one window for all content. I even deleted all the CHMs from the parent and regenerated all of the help projects, using a command prompt build, to an external folder and it still worked ok. The HHP file list all of the merged help as relative paths. All is well with the world, finally.
Now the devil in the ointment
I have a parent project that is about 75% common to two products. I therefore use two TOCs which are also about 75% common to compile two different version of the parent CHM. in different locations.
I used TOC (A) to remerge all the original child CHMs and produce A.chm using A.ssl
I then imported TOC (B) and while I expected some of them to fail, I compiled the help anyway, using TOC (B) and B.ssl just to see what else needed fixing.
NIGHTMARE, every link to merged help, in B.chm opened in it its own window. Worse than that, when I compile A.chm again they also open in seperate windows also.
On inspecting the HHP file, the [MERGED HELP] section has gone again!!!!!!!!!!!
This is probably down to my ignorance but I didn't expect that importing a second TOC, with links to merged help that were made in the first TOC, would undo those references that you have just fixed! I only used TOC (A) on its own because I was fed up rebuilding the project so many times.
The warning, and I appologise if this seems obvious but it wasn't to me, so...
When recreating a project and importing/reimporting the original files, ALWAYS import/have all of your TOCs in place before you remerge CHM files. Re-importing another TOC will overwrite the links.