Two projects will mean that every time something common changes you have to change it in two places. Quite apart from duplicating the work, that is prone to error. RoboHelp enables you to single source different outputs. You tag the content to control what is in each output.
You set up tags for content you don't want in Output 1 and tags for content you don't want in Output 2, then apply a build expression in each output to exclude unwanted content.