I need to change how payments are applied to invoices.

ApplyPolicyPayments() looks promising! Make changes to the method to look at the bills in order of the invoice due dates.

Run a test on the DEV environment, and the system is still exhibiting the same bug.

At this point, I wrote a quick logging plugin that I could attach to the DLL and start telling me what is going on.

Turns out, payments are actually applied in a method named BalancePolicy(). So what does ApplyPolicyPayments() do? It DOES apply payments to bills, but then just doesn't save the work. Having it commit the transactions breaks the billing system. FML.