Hi I phoned the Standard Bank Centurion branch where I wanted to do the biometrics and explained what was happening. They were very helpful and put me through to the Home Affairs offical who was working in the Home Affairs office at the bank. I explained the situation and they asked me what time I wanted to come through and told me to come through with proof of payment (from Home affairs website and bank statement showing payment). Just note, because they manually have to mark you off as having paid, it takes longer than other people who went through online but it's still much faster than actually going to Home Affairs. And it only took 4 days for me to get my passport after. Good luck
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