Starting with RH6, you have the option of using RoboHelp's
command line compile, rhcl. I have started using it for our RH6
help projects, and am pleased with the results.
The command line compile allows you to specify an output
location that is different than the one listed in your SSL, which
is very convenient.
There is one bug that you might run into: if you copy the
source projects to a new location before performing the command
line compile, there's a path in the project.pss file that does not
update correctly. It's the Language line. It sometimes (but not
always

) retains its original path. As a result, the rhcl
process reports a bunch of errors at the end. My workaround was to
place a replica of the "missing" file (robohhre.lng) in the
expected location. Kludgy, but it works.
Using the command line compile, automating your process
should be do-able. You might have to play with it for a bit to get
the results you want, but it's pretty straightforward.
G