You know, I thought I had added that ability but apparently I only provided the ability to add symbols.
It's not an easy thing to do because symbols are read only in the PDB. It requires a "new" part being built, the information copied over to the new part from the old part, and removing the symbols at that time. The problem with this is, as it sometimes happens with Heal PDB, the pin mapping doesn't want to commit the same way it originally was added. This is because parts that have been translated can bypass the internal checks that automation can not bypass.
You can send an email to my bosses: Jody Miller (Jody_Miller@mentor.com) or Scott Williams (Scott_Williams@mentor.com) and see if my priorities can be changed to add this capability. Otherwise alternate automation would need to be created to allow for this type of modification.