New challenges in aerodynamic design of flight vehicles are sometimes met by changing the wing sweep angle during flight. Simulations of the wing deployment or folding process should include aeroelastic dynamic loads analysis for structural and mechanical design. The presented work expands common aeroelastic procedures to simulate the morphing process using the Increased Order Modeling approach. The analyzed case is response to gust excitation during rapid change of the wing sweep angle. A frequency-domain dynamic gust response is first performed for a nominal sweep angle with the wing and body components represented by separate model coordinates that are coupled to satisfy the interface displacement compatibility. A time marching simulation is then performed to modify the nominal response in a way that takes into account the changing external excitation, structural and aerodynamic effects. Each time step involves modifications of the interface compatibility constraints, the unsteady aerodynamic force coefficients and the gust incidence angles, using a previously acquired database. The process returns to frequency-domain formulation for final calculation of the structural response and dynamic loads.