I asked ISN and they replied:

"The only option we have available to decide which orders qualify for flex fund is through the Services & Inspection Types check boxes in the Flex Fund options.

This means we can allow only orders using specific services/inspection types to utilize FF.

We are, currently, unable to disqualify an order from flex fund based on a discount being applied."

We would LOVE if this was automated for us because at least once a week we run into the issue where Flexfund gets applied on an order that contains a discount. Usually the inspection has already occurred and it involves the client already having received their report, deciding to pay instead and removing Flexfund... which delays the payment and costs us time trying to get Guardian to cancel their order. Please add a feature that we can enable to stop this from happening. Thank you!!