Flow control devices are used within complex intakes to reduce the flow distortion which can adversely impact the stability and performance of embedded engines. There is a need to assess the capability of modern computational methods such as detached eddy based models to compute the unsteady flowfield and to evaluate the potential benefits of flow control devices on the unsteady distortion. This paper investigates the unsteady flowfield for an S-duct using Zonal Detached Eddy Simulations (ZDES) with passive flow control devices modelled with an overlapping Chimera grid method. The ability of ZDES to evaluate the impact of passive flow control devices on the unsteady flow distortion was assessed. The computed unsteady flowfield at the Aerodynamic Interface Plane was compared with experimental data based on total pressure and velocity field measurements. For the baseline configuration, the ZDES model has proven to be able to simulate the unsteady flowfield at the AIP, to provide the time averaged and fluctuating levels of swirl distortion within 1% and 13% respectively of the measurements. The strong impact of the flow control devices on the AIP flowfield was also captured by the ZDES. The overall increase of pressure ratio (PR) at the AIP due to the flow control devices was predicted with less than 1% error. The 65% reduction in swirl distortion fluctuation when the flow control devices are used was predicted within less than 8% error by the ZDES compared with S-PIV measurements. Overall it was determined that the ZDES method is able to simulate the unsteady flow and distortion characteristics for both the baseline reference configuration as well as the case with flow control.