which 'factory settings' are you expecting to find? I think you're saying that the values in hand written ink have come off...
Can you read the parameters that goes with the missing values?
On some California gasoline powered engines for instance, it's not unusual for the factory or dealership to change ignition timing before delivery, or even during first service (pursuant to a factory service bulletin), compared to the 49 state engines.
1995 E350 7.3 Diesel, 4x4 high roof camper, UJOR 4" lift