Pen and Ink Pro 2.4 (PIP2, SP4) can't even edit it's own work, let alone anything made w/ previous versions. You have to buy an additional 'Whiteout' module, and even that never really seems to do an entirely suitable job of it.
Magic Marker does OK (unless you have the Permanency plug in installed); but that's limited to certain types of surfaces, of course.
Pencil 3.2, w/ Eraser 2.1 add-on installed, however, can still edit work that was done w/ Pencil 1. I do hear that even good old Pencil has some trouble with the Colors Pack.

Friends don't let friends use booleans.