Note that I am talking about the "fairing" that serves as the basis for the constructive drawings of the structure. I am not talking about the body lines plan of the conceptual project, which is always much less exact, it does not need as much precision.
The normal thing, indeed, is to start defining the body lines plan through a series of cross sections and through the longitudinal profile (if, in addition, you have the points of the sheer line, better than better). With that base, buttocks, water lines or diagonals are traced, until the shapes are smoothed. For me, none of these lines is more important than the others, but it is very true that in the initial drawing, it is very normal to forget about the diagonals. I would not say that the last thing I draw are the water lines, on the contrary, the last thing I take for granted are the cross sections, which are the ones that will allow me to build the real frames of the ship.
Regarding your question, when a point on a line is moved, what is actually moving is a point on the surface of the hull, thus a change in a "secondary" line (as perhaps you would consider it) of course which will make me change the frame or any other "main" line. As I say, for me, all the lines are equally important and none influence more or less than the others on the smoothed shapes.
And I insist, imo, in this work, hydrodynamics, or the lines of water flow, do not intervene at any time.