Any issues would really depend on how much you have CA PPM integrated with your HR systems ; its these interfaces that would be affected rather than any stock PPM functionality.
I would GUESS that you would need to update the identifier in PPM to match your new HR regime. But its also conceivable that that "mapping" is handled in the interface between the two systems (so it becomes an interface issue not a PPM/identifier issue).
If you are using this "HR ref" as the PPM user name, then you will probably have issues trying to update this through XOG (since it is the primary key/unique identifier), but you should be able to update it in the application itself. If the "HR ref" is just a piece of information held against the user/resource in PPM, then you will be able to update it en-mass thru XOG.
So its really hard to say whether you are going to have "issues" without understanding your interfaces / how you have implemented PPM.