This work develops the so-called compensated impedance boundary conditions that enable stable time domain simulations of sound propagation in a lined duct with uniform mean flow, which has important practical interest for noise emission by aero-engines. The proposed method is developed analytically from an unusual perspective of control that shows impedance boundary conditions act as closed-loop feedbacks to an overall duct acoustic system. It turns out that those numerical instabilities of time domain simulations are caused by deficient phase margins of the corresponding control-oriented model. A particular instability of very low frequencies in the presence of steady uniform background mean flow, in addition to the well known high frequency numerical instabilities at the grid size, can be identified using this analysis approach. Stable time domain impedance boundary conditions can be formulated by including appropriate phaselead compensators to achieve desired phase margins. The compensated impedance boundary conditions can be simply designed with no empirical parameter, straightforwardly integrated with ordinary linear acoustic models, and efficiently calculated with no need of resolving sheared boundary layers. The proposed boundary conditions are validated by comparing against asymptotic solutions of spinning modal sound propagation in a duct with a hard-soft interface and reasonable agreement is achieved.