[Indivio]

I had this very same problem and couldn't figure out how to solve it. Finally, I looked under Preferences, Data. At the very bottom, there is a checkbox -
In Context Mode: Show Projects and Action Groups.

This was checked. I unchecked it and voilà all the empty projects disappeared from both Context Mode and Available Perspective.

I know this reply is a year later, but hopefully it helps someone :)