Are your load primarily in-plane, membrane loads, or are your panels actually bending?
I ask this because if you are entering loads through the User loads and your loads are primarily membrane loads, you might be able to get away without shifting the reference plane.
If you leave the Mx, My and Mxy as “constrained” on the FBD tab and just enter the Nx, Ny, Nxy from your solution, then HyperSizer will apply your membrane loads and then will calculate the necessary bending loads to keep the panel from bending. This would be like a uniform end shortening solution. When you shift the reference plane of a panel, the membrane loads (Nx, Ny, etc) do not need to change, but the Mx and My do. However, if your panels are assumed to be loaded primarily in membrane and are not bending, then this approach could work quite nicely.
If you have substantial panel bending going on, however, this will not work. If that is the case, then you will have to shift the reference plane by calculating new moments at HyperSizer’s reference plane, or, we will have to change HyperSizer to allow you to shift the reference plane.
Phil