Each airborne flight has only one flightplan, which was submitted for that particular flight.
The routing is embedded into that flightplan and only that one routing is valid for that flight.
In case the routing is no longer available for the next flight due to airspace closure via NOTAM or airways being restricted by time of flight / day of flight, another routing will be used for that flight and submitted in the flightplan.
In case the routing needs to be changed for an already airborne flight, a new IFR clearance is read to the crew en-route, which alters the existing flightplan.
Alternate routings are usually managed by the airline's dispatch / planning centre and the best routing for a specific flight is created by the dispatchers, taking into account weather, NOTAMS, restrictions and many other factors.
En-route changes to a flightplan are made by ATC units and their data processing centres, if an impromptu change needs to be made due to airspace closures or other restrictions coming into effect which were unforseen.