Well, you have a problem lol. What i do is i repetivly press save like 10 times just to make sure. To many times have i made a half-map, saved it, re-loaded it, made the full map, saved it again and it reverts back to a half-built map.
Anyway If the change is predictable then just off set your peices slightly so that when it's loaded in a game the shift INTO place. either that or make sure that while your forging that you have the Phase tool selcted not fixed or normal. lol