There is not enough information about the 2 PHl agents being set forth here to know whether or not they have been habitually waiving fees and honoring expired airfares. I suspect the software you speak of red flags any agent who repeatedly makes too many concessions within a certain time period.
If a reservation has cancelled due to an agent error, it should be OK to reconstruct and honor the airfare the customer contracted for. But if the customer forgets to call back and ticket in time and their reservation has cancelled, then the customer needs to pay the fare in effect that day. Sometimes you will get a lower fare by creating a brand new reservation instead of working in the cancelled one. If the fare is still higher, then that is what they pay.
If a reservation has cancelled due to an agent error, it should be OK to reconstruct and honor the airfare the customer contracted for. But if the customer forgets to call back and ticket in time and their reservation has cancelled, then the customer needs to pay the fare in effect that day. Sometimes you will get a lower fare by creating a brand new reservation instead of working in the cancelled one. If the fare is still higher, then that is what they pay.