This usually happens when the 500mm high wall is raised above 1.5m from the zero level of the story (I hope thats the case for you). So before you raise that short wall from zero, go to settings of the wall under floor plan and section, change floor plan display from "projected" to "projected with overhead". Once you do this, the wall wont just disappear, it will be represented as dotted on the home story. I hope this is clear and fixes it for u