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Are you using RoboHelp Server and WebHelp or FlashHelp Pro output? If so, I believe there is a setting you may be able to change using the Configuration Manager that determines whether all projects published to the RoboHelp Server are automatically merged or not. It sounds as if you are wanting to publish multiple projects to the RoboHelp Server, yet treat them as individual projects without merging.
I use RH6 Sever and have never used RHX5 Server. However in RH6 Server, launch the Configuration Manager (I believe this is the same in RHX5 Server) and click the Projects icon on the left hand side. In there is a "Automatically merge projects of same type" option.