There is no native connection between Bill A and Payment C that you can use. This is not due to NetSuite's EBP, the data structure would be identical if you applied the credit and made payment through the Pay Bills page or manually. You could probably get a script written to use the Payment File Administration to relate them, but that seems like a lot of cost for the benefit.
Can you instead pull an AP payment history report or a saved search that shows AP transactions and share that with the vendor as backup?