Hi
@m.m.m ,
The first idea that comes into my mind is that you must have changed your symbol manually after modifying the schematic which may have led to the problems in pin order. You can try to open your schematic view, do Check and Save and after that go to Create -> Cellview -> From cellview and in pop-up menu click "modify". It should suggest you to update the CDF order as well and after that the port order should be fixed.
Alternatively, you might go to (in CIW): Tools -> CDF -> Edit.. and fix it directly from CDF manager.
Hopefully, that helps.