Thanks for your insights, Patricia.

Because the terms code was defined to offer a discount only for 10 days, generating the payment list in system checks 12 days later will follow those rules and not offer to automatically deduct the discount. It can be edited manually. That technically part is everything here.

Ideally this would have been caught on the check run on Sept 5, but the rules also state that if the sum of the generated transactions (invoices, unapplied credits, prepayments, etc) is zero or less for a vendor, then a check is not issued. If the credit note was meant to be completely independent to the invoice, current program behaviour cannot differentiate that. If the credit note was not meant to get in the way of paying that invoice early and getting the discount, it needed to be taken off the payment list as I believe Patricia was trying to assist with.

You could also have used Payment Control to edit the Discount Date of that first invoice to Sept 13 and get the discount included. But that also takes a manual step.
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Are you looking for a feature enhancement to system checks, to generate the payment list in a different way? Such as an option to not load unapplied credit notes or prepayments in the pre-check register? Or something different? I'm thinking of areas that would have made the Sept 5 check run be able to pay the invoice, rather than areas for the Sept 12 check run to ignore the Terms Code rules. We're working on Payables 9.3B right now.