The historic locomotive is taking part in four special tours this month with the A1 Steam Locomotive Trust-owned Tornado, the first time the two iconic engines have ever worked together on the mainline.
For the October 28 journey, the Scotsman was due to join the train at York after it had collected passengers at Peterborough, Newark and Doncaster under 'modern traction'.
It was then due to haul the vintage carriages to Leeds via Church Fenton and Garforth to and then onwards to Skipton, Settle and Carlisle.
Instead a diesel locomotive has been used as a replacement engine and has been photographed in the Church Fenton area.
Tornado is still due to work the return journey from Carlisle back to York.
The news will disappoint passengers with tickets for the excursion as well as trainspotters lining the route to see it.
The Scotsman operated the return Carlisle-York leg of journey from Middlesbrough, Yarm, Thirsk and York to Carlisle yesterday without incident, though one witness claimed the engine appeared to be struggling as it approached York.
Matthew Cox said: "I was at Sherburn last night and it stopped between Sherburn and Milford and the crew were out looking down the side near the front. When it set off again it sounded very rough as though the timing was going."