How to merge projects is covered in detail on my site. It may be though that the way the links have been set up will not be the same way links would ordinarily be set up in merged help.
For that reason you might want to consider other options.
1] Link the Framemaker content to Project B. That however would also likely have link issues.
2] Use something like ZoomSearch instead of RoboHelp's search. That would be run against the output that you are already creating. ZoomSearch is also covered on my site.
See www.grainge.org for RoboHelp and Authoring tips
I got a tip via email to do this:
- close RoboHelp
- back up everything
- delete project A's.xpj
- add the [FILES] entries from B's .hhp file to A's .hhp
- copy the content directories from B to A
- open A's .hhp in RoboHelp and it will automatically create a new .xpj
Fast and easy. I'm a bit dumbfounded that in 2012 I'm still editing .hhp files, but whatever gets the job done.
I can't draw any general conclusions based on this. There were no internal links in any of the topics in the RoboHelp project B. There were "go to URL" hypertext links in the FrameMaker project A to HTML files generated by project B and manually copied into A's WebHelp output.
I don't know why it was set up that weird way, I suppose it was a kludge to merge the output from the two projects. My .hhp-merged project generated files of the same names in the same directories, so it worked fine.