When you say Grade Tolerance what do you mean - the breakline approximation parameters?
Are you sure you don't have a selection set applied to your view filters or something like that that is hiding the lines or that you turned off cad visibility in the advanced view filters setting
If you select by layer and choose a layer that has the disappearing linework on it and then look at selection explorer and see what is selected pre the change and then make the change and repeat - select by layer will pick hidden and unbidden data and will tell you if the data is being deleted or just being hidden for some reason
I would be surprised if we delete the lines and I have not seen that personally but you never know - I would need the file and the steps you take to recreate the problem
Alan