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I'm by no means an expert...
You should create a folder through the RH interface not Explorer. That way the folder will be registered with the fpj file that determines what files/folders to display.
It's not wise to perform 'covert' file ops in RH...use the interface whenever possible.
FYI, even if RH does display the folder you create, I highly doubt it will display the word docs within it. Maybe they should be baggage files instead...
RH only sees the folders and files that you create via Project Manager. They are recorded in RH's database, the CPD file. If you don't add them that way, they are not part of the project.
It is also important the project is on your hard disk. The database is a Microsoft Access database and they don't work well across networks.
To help clarify "why?" It is because you are creating a CHM or webhelp system, so RoboHelp creates virtual folders that will be the folders in the built project. They don't need to exist on your computer.