Why do airliners have to file delays through their handlers?
Since you mention Dublin, I am going to give an answer that describes the situation in Europe. Other parts of the world may have different procedures, although I believe they will be similar. 

Usually a flight plan must be activated within a given time window to ensure that there is enough capacity (airspace, ATC staffing, departure &amp; arrival airport constraints) along the route to handle the flight. If the flight is not departing with this 'slot' a new flight plan needs to be requested and approved by the Network Manager Operations Centre (NMOC) (Previously called Central Flow Management Unit (CFMU)). 

The controller is not responsible for filing flight plans and cannot be tasked with doing the paperwork for the crew. The crew therefore needs to contact their handler or flight operation centre to refile a flight plan. 

The NMOC will reassess the flight plan and verify that there is capacity along the planned route to handle the flight. If there isn't, the flight may need to be planned along another route or an additional slot delay will be given.