It is not clear why you need to change anything from what I read.
You had a RoboHelp project with its own content plus linked Fm files. From that you generated both WebHelp and PDFs. Now you don't need the PDFs. That would suggest you just stop generating the PDFs from RoboHelp and nothing else needs to change.
Maybe you were you generating those the PDFs from Framemaker? If that was the case, you could again just leave things as they are and create only the WebHelp from RoboHelp.
If you no long want to use Framemaker, it depends on whether the content there will change in the future. If it will not, then again, you can leave things as they are. If the content will change and you want to edit in RoboHelp, then you will need to unlink the files and import them instead.
See www.grainge.org for RoboHelp and Authoring information. $£0.00

@petergrainge
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