If a student has two UPNs you would need to get advice from your Local Authority as to which one to keep.
If the student has come from another previous school, you could also check with their previous school which UPN they used if they still have that information.
Please refer to the Department for Education (DfE) guidance regarding issuing of permanent and temporary UPNs): Unique Pupil Numbers (UPNs): a guide for schools and local authorities