A lot depends upon exactly what you are trying to do. For Delta to take over the booking and do itinerary changes, they charge (or they are supposed to charge) the $50.00 fee. If you are upgrading with miles or certs type of situation or similar without changing the routing, they do not charge a fee since agencies are not allowed to those upgrades. As people have noted, they have been successful in getting the fee waived. The agency does lose control of the booking and can no longer do anything with the new tickets, although they should see the changes to the itinerary in their GDS. As far as handling changes due to a schedule change. The agency has some latitude on new flights and can call Delta if necessary to get assistance. Delta will give the agency the option of reissuing the tickets (In which the agency keeps control of the PNR and tickets) or they can have Delta handle the reissue (which the agency then relinquishes control).