I believe you do it like this. In the work plan of the Portfolio select the required project. On the Misc menu select Detach. This will turn the selected project into a standalone project.
How do I move a project out of a portfolio to be a stand alone project?
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That works - I found the detach option under the "Other Actions" menu.
I believe this information has changed. I was testing this out today and could not find a Misc menu or Detach option anywhere. I did simply select a project I wanted to remove from the portfolio and chose the Delete option which asked if I was sure I wanted to delete the selected shortcut. I answered yes and the link to the project was removed from my Portfolio project. I verified the project whose shortcut I deleted still existed (it did.)