AP Discount Terms issue

Hi Everyone,

Bear with me, I'm a developer playing a functional lead for the week, so I don't know all of the AP lingo.  In a nutshell, the issue is that a discount is taken as if we pay by the discount date, but in many cases the pay cycle is after the discount date and hence we don't get the discount.   So in this scenario, what is the best way to get the lost discount charged back to the deparment.  Or, this there a proactive way to flag this payment as discount taken to move it along faster in the pay process. In case I didn't