Hi Faisal,
I am facing a very similar issue. That is, I want to edit the Personnel number on an Employee business partner in CRM, which was created when the employee was downloaded from ECC.
Specifically, just like you, I want to remove the Personnel number from one Employee BP, and maintain that Personnel number on a second Employee BP (both BPs were created by replication of employee data from ECC).
Did you ever find a solution for this?
(The reason I want to do this, is that a duplicate Employee BP was inadvertently created when sending an org model transport to CRM production and then subsequently running PFAL in ECC production.)
Thanks,
Jeremiah