The term gets its meaning from the context of the source you referenced: a part of the particular management system used by Subway restaurant franchises.
A restaurant's profit or loss is determined in part by the cost of raw ingredients, in relation to the total sales receipts for all the food that is ultimately sold. Anytime something must be discarded instead of being sold, it reduces the profitability.
Apparently, Subway's management system makes allowances when bread is discarded, to offset the loss by compensating the franchise operator with some sort of credit. By doing this, it encourages the operator to always use freshly baked bread, and thus, maintain a consistent quality in all store locations.
So, as your example sentence says, the franchise inspectors look at the "discard credits" in the management reports as a way to see that the store is following the rules, and discarding a certain amount of unused bread each day.