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The short answer is indeed you may create context-sensitive help files for C# applications.
The long answer is that RoboHelp is simply one of a few different tools that you may use for this purpose. Just as you might use a power saw to assist in building either a garden shed or a shopping mall, RoboHelp might be used to create a help file for any number of applications. It's not the application that matters here. Rather, it's the knowledge of what you need to do and where you make the changes that counts.
I think your confusion is stemming from the change from C++ to .NET. As I understand it, only if you wish to run the help as something called a "service", you can probably use basic RoboHelp to create your help. I think there is something called a "DotNet API" that you may wish to look at.
May we assume you have RoboHelp 6? If so, have you perused the information you find by clicking the following books?
--->Information for developers
------>Programming Help for .NET
Sorry, but that's about where my knowledge will drop off. I'm fairly weak in the area of CSH, for the simple reason I've never been presented with an opportunity to work with it day in and day out.
Hopefully others will chime in here to either confirm or deny what I've posted.
The simplest way is to call a topic URL from the application, without the need for APIs. For example, the MyUserMainFrm form (the main User Configuration window) would call your MyUserMainFrm.htm topic. If your help is merged, you and the developers can set up an alias file (we call ours form_path.txt) that will point each call to the proper child project folder name (such as MyUserMainFrm, mergedProjects\UserChildProjectFolder).