Moment of Inertias aren't defined for shells any where, only the thickess is defined as a shell property. If you're referring to beam elements, then that's a different matter.
I don't see section stiffness matrix anywhere unless you are creating your own user element.
If you alter the moment of inertia of a shell without changing the area then you must alter the shell thickness as well as the width. In that case you are then altering the shape of the model.
If on the other hand you add beams to the shells then I can not see how you are modelling the part physically correct. In finite elements you should expect to get a reasonable model of the geometry. I don't think what you are attempting will in any way be a proper representation of the real thing.
