Hi Karthikeyan,
Can you check whether the FM BBP_PD_PO_DB_DELETE is of any help. This is used to delete the PO itself. You can check whether it is possible with this FM to delete the change version.
Try to give the GUID of the change version and delete the same.
Just a try with this workaround. Not sure whether it will actually work out.
Regards
Pramod