our office have just encountered this - we have a pretty messy early-stage schematic design model of a campus with different buildings and multiple design option sets, each with several design options for differing level heights for the different buildings. We now have to reduce the ground floor level height of one of the buildings across all design options, so all of the levels above need to move down as well. Trying this results in an error that essentially forces us to delete all model elements of one of the design options as well as the corresponding ground floors.
Conclusion: Design options with differing story heights are a bad idea. You have to either create completely separate level sets for each design option and hide them via filters, or you start a completely new model for every option.
This is making early stage design work very tedious. Maybe it would be a good idea to be able to move levels to a specific design option.....