WCR supplied film-maker Warner Bros with the locomotive and carriages for the Hogwarts Express in the Harry Potter film series.
The West Highland Line’s historic Glenfinnan Viaduct also featured.
The rail journey has been described as one of the world’s most scenic, and is popular with railway enthusiasts as well as film fans.
WCR was in a long-running dispute with the ORR about having to install central locking on its Mark 1 carriages to prevent passengers from opening doors when the train is moving.
Boss James Shuttleworth told BBC Scotland News the system would be installed, but this would take time and it had applied for an exemption to use the carriages meantime.
He said exemptions had been successfully secured in the past, with stewards manually locking doors.
Shuttleworth said for a few seasons it had used more modern Mark 2 carriages, which have central locking.
But he said a decision had been made not use them this season because of their reduced capacity, and that they also require a diesel locomotive at the back to provide power to an air conditioning system.
He said using Mark 2s had resulted in lost income, and customer feedback showed a preference for the Mark 1 carriages.
Shuttleworth said details on the start of the new season would be released as soon as they were available.
The ORR said no agreement had been reached on an exemption and the application was being reviewed.