Yes, might be.
But Source or HR Team need to inform bw team to delete the Employee which has been deleted from SAP.
When user/client request to delete an employee from SAP, Source team need to inform the same to bw team. Later bw team will delete particular PERNR(Employee).
While deleting PERNR in BW side, BW Team need to make proper steps(target names where PERNR have been used).
that doc will be helpful in future.