How can I lend my son's company $50,000 to pay a Tax Bill, so that the payment from our company's books is coded correctly (ie not as a purchase or operating cost), and the repayments from him are also coded correctly (i.e. NOT as income) so that the NZ Tax requirements are satisfied?

You would show the transactions as a loan with your company acquiring an asset and when money is repaid it reduces the value of the asset and is not recorded as revenue. No doubt you will need to declare the value of such assets