Changing design using SM mode when you already have that designed built and in service will give you some bugs, such as ship wont have the same max speed as in the new design if you upgrade engines or whatever, some ship statistic are save with a per-ship basis, while some system use the *reserched* tech. I.E.: you change the fire control system it will use the new fire control as its not saved with the ship information.
Ship information saved goes as follow (list not complete and will not be to prevent spoiler or abuse) Thermal Emission, Ship cross section, Current and max shield, Crew grade point, Fleet trainning points, current reactor power and some others . If you change design that affect any of these value and some other not-state it wont affect those already built wich cant cause a headach trying to figure out after a while who is what, Mk1? or s-med Mk2?
This i hope will solve some question reguarding modifying design with SM, its good if you want to change something at last minute while you are building it, but as soon its out of the shipyard it may not update every piece of data.