Pre-load.
Bearing in machinery are designed to run with a given amount of pressure on the sidewalls for them to run properly. It's commonest (and most critical) with cone bearings which can be thought of as three wedges (inner, outer race and the tapered bearings) working against each other. Too much preload (Torque) and the wedges bind. Not enough and the bearings are loose and can get slightly sideways changing the angle of their wedge shape. The bearing will start binding, wearing and heating the bearing at an increasing speed. In general when bearings are loose, the shaft can wobble around which transmits energy from the shaft by it's flopping motion to the bearings/races, which in turn heats things up and it's downhill from there.
Marking the nut and the input shaft when replacing a flange will put the preload on the bearing very close to what was when it 1. Left the factory, 2. was last rebuilt. You are trusting that they had it right. If the diff. is know to have a lot of miles on it, that is a very safe assumption.
If you really want to dial it in. Determine if the replacement flange is thicker or thinner and adjust the angle between the marks on the nut and the shaft to compensate for the difference. So if the replacement flange is 0.25mm smaller and thread pitch of the shaft is 1.0mm, then you would turn the nut a quarter turn past the matching mark point. (I don't know what the true pitch of the shaft is, don't bet your rear end on 1.0mm.)
Don't sweat it, the real difference in the flange thicknesses isn't such that the torque values would be outside the tolerance of the bearing's recommended amount. I don't think fine German engineers would neglect to think of that when writing the tolerances for the flange thicknesses.
At the factory, the nuts are put on with torque drivers that are regularly tested to ensure the proper torque being used. When you move into that world you will start hearing words like 'running torque', 'static torque' etc. That is why using the torque value to loosen the nut is not the value used to torque it on. Cleaning and greasing will greatly affect those numbers.
More than you probably wanted to know, but I just had to say it.
Cheers,
Ned