Impedance eduction of acoustic liners is commonly implemented under the hypothesis of uniform mean flow by applying Ingard-Myers boundary condition at the lined wall. However, flows in ducts are intrinsically sheared, and it is reasonable to question the validity of the uniform flow hypothesis, especially when considering large ducts, high-order acoustic modes and flow velocities representative of aircraft nacelles. This paper studies the effects of shear flow in such a framework. A numerical multimodal method computes the acoustic modes and the acoustic pressure field in a 2D lined duct with shear flow. Then, an eduction procedure taking the flow profile into account is introduced. The performance of the latter is numerically compared against results obtained using the uniform flow assumption. A significant gain in robustness is demonstrated, in particular for ducts with large cross-sections, high-speed flows and upstream propagating waves.