What to do?

[Cerseilannisterinthesnow]

I've just had the whole clutch and associated parts changed at the garage after the clutch plate went to bits on my 11 plate cmax which you usually press the clutch to start it but now you have to press both clutch and brake to start. Will this sort itself out after so many starts or will it need restored at ford?

Since about 2014 Ford Transits won't start without both brake and clutch pedals being pressed. My guess is that the garage has updated your software and this is a consequence, in which case this is your future.