A slight variation on the various threads we have about his dying during the war but suppose that Churchill via the vagaries of fate, his cousin the 10th Duke lives longer but dies without an heir or his nephews predecease him, inherited the title of Duke of Marlborough in mid-1944. Whilst I can't see people wanting to change horse at that stage so he remains Prime Minister it does cause complications as his elevation, or depending on your views demotion, to another place means that he's now unable to speak in the House.
My general thinking was Churchill stays as PM, Attlee remains as Deputy PM, and someone in the Commons is elected as the new Leader of the Conservative Party, a position along the lines of First Secretary of State is created to give them precedence, and they speak in Churchill's stead. This neatly sets them up for the post-war general election. Other than the obvious choice of Eden would there be any other candidates that might have been able to steal it?