I think it's partially related to the .hcc file in the master
project.
My company recently had a consultant come in to do a day's
training, and he knew his stuff.
I've been merging HMTL projects, and seeing the TOC's in the
merged project were subtly modified from the original sub-project.
When the consultant looked at it he said there were errors in
the logic in the HTML within the master TOC. Specifically he said
that not all <ul> and <li> statements were being
properly closed off, which is why some topics in the sub project
were appearing as books in the master when that was compiled.
(He's looking at the problem at the moment).
My HTML knowlege is pretty basic, but if anyone wants to see
the problem, create a sub-project with a TOC nested to at least two
levels and associated t.opics. Merge that project into a master
with the sub project as a child of a master topic TOC book and look
at the compiled output. You should see that some of the sub-project
topics now appear as books. Go back into the master project .hhc
file and you might be able to track the associated logic problems -
the consultant thought it was a RoboHelp bug.