I don't have proof of this, but I was under the impression that shifted lines were never exported with the data to be imported later. 


If you have a headland guidance line made with an ATV, it gets shifted over for say a 40' planter, 100' sprayer, 75' spreader, and who knows what else. You don't get all those different parallel lines back into the computer. You still just have the original. The same would be if you were in those machines and once the line was shifted for the new machine width, you then hit the manual shift button a few inches here or there. I don't think that's coming back into the computer as a new line or overwriting the old line a few inches off. 

My thought which could be wrong was, the saved line is saved. Any shifting you do in the field won't impact that original line saved on the computer.