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Welcome to the forum.
As you are talking about a source file (singular) I guess you are using RH for Word rather than RH HTML.
It should be possible by creating one TOC that is the total of the two you want. By applying conditional tags to topics, when generating you can exclude those topics from a build and you will get the TOC for what is included.
Create a small project with some dummy topics to get your mind around how it works.
I used the term source file because I've haven't used Robohelp in 6 or so years, so I started with a Word file and imported it into RH HTML. Not the best way to do things, as I found out the hard way.
I have all my topics in one RH HTML project now, and I need to create a Webhelp file, an HTML Help file, and a printed document from the project.
Not sure what response you are looking for as what I described will work for RH HTML, assuming you have regained your sanity since importing the Word file!
It looks like to me that you are talking about outputs. If that's the case, the answer is yes, you can generate HTML Help, WebHelp, and Print Documentation outputs all from the same RoboHelp project.
In the Project Manager, there is a folder called "Single Source Layouts." Expand the folder to show the different layouts. Double-click on a layout to open a dialog where you specify the directory where your output will be stored and other things. I believe that if you do this once for each of the three outputs you want, after that you can go to File > Batch Generate, and RoboHelp allows you to run all three together instead of having to open each of the three dialogs every time you want to re-generate the three outputs. I use only one output, though, so someone else may be able to give you more information on the batch generate function.