A second or even a thrid SA passport is not an issue.
You go to Home Affairs Passport office.They may or may not ask for your pilot certificate.You fill in the forms pay them and TWO WEEKS later you will get a sms "Passport ready for collection"
By SA law you may posess 3 passports as a crew member under Maritime law.
Just make very sure you do not go back and tell them you lost one-Priviledge withdrawn at the desk where you are making the statement