To the best of my knowledge the command line can only be used
to generate what is in the project, not add to it. Combine that
with the fact that a merge within a merge is a nightmare, if not
impossible, and it looks like you really need to be reconsidering
the approach.
Well, you can add files to a project in source control from
the command line, although my experience with adding files using
the RoboSource Control rather than RoboHTML has been less than
encouraging.
Thanks for your help, you've saved me many hours down a long
dark road.