I agree with Višnja Svrdlan, I have not found a solution to this problem, I build my 3d only with Project Zero reference level and when some of the objects disappear I do that, with the symbolic cut.
Although, if the height difference is not much, eg 1m. you can set the Story zero level to 0.50 for the ground floor to be somewhere in the middle, but I thins it is much more confusing.
Use the zero of the ground level on site as the project zero and you ll be fine.