Here is a workaround:
Draw a rectangle over the top of the viewport in paperspace.
Use QUICKSELECT to select only the viewport.
Start the Viewport Clip command (VPCLIP).
It will already have the viewport selected and will prompt you to select the object to clip with.
Select the rectangle.
Voila! You should have a workable viewport.
You can use quick select to select all the viewports, then holding the Shift Key, pick the viewports you want to 'unselect', leaving the phantom viewport for the VPORTCLIP. Your properties manager dialog box will show how many items are selected, so leave the Properties Manager up and open. The phantom viewport will not show with grips. You will only know you have it selected by looking at the Properties Manager. If you have more than one phantom viewport, you're screwed. :-( You may just have to erase the phantom viewports and re-create them (or the one that you want).