If anyone else is experiencing this issue , here's the response from Technical Support:
Open your Second Floor Plan and perform a Cleanup. This should correct the roof for this project. There are two issues related to Multiple Floor Roof at this time: 1) if you turn off Multiple Floor Roof, then back on again, you will need to perform a Cleanup (this was the current condition of this project). 2) if you modify a wall height on a main floor wall that is referenced by a second floor roof, you will need to close all 3D views and reopen them to see the roof generate completely (a system reboot not necessary). Both of these issues are currently being reviewed by development.
I'm pretty certain I may need to refer to this a few times in the next few days.