Eulerian Embedded Boundary Methods (EBMs) for Computational Fluid Dynamics (CFD) are particularly attractive for complex fluid-structure interaction (FSI) problems such as those involving large structural motions and deformations, or topological changes, and for which the alternative Arbitrary Lagrangian-Eulerian (ALE) methods are simply unfeasible because of mesh crossovers. However for viscous flows, EBMs also face many challenges. Chief among them is the fact that they do not track the boundary layers around dynamic rigid or flexible bodies, essentially because they are Eulerian methods. As a result, their application to viscous FSI problems requires either high mesh resolutions in large percentages of the computational fluid domain in order to capture at all times the viscous effects, or adaptive mesh refinement. Unfortunately, these two options are either computationally inefficient, or labor intensive. For this reason, this paper proposes a simple and yet computationally reasonable alternative for maintaining the boundary layers resolved throughout the simulation using an EBM of a turbulent viscous flow past a dynamic body. In this alternative, the underlying non body-fitted mesh is rigidly translated and/or rotated to track the rigid component of the motion of the dynamic obstacle, the flow computations away from the embedded surface are performed using an ALE approach, and the wall boundary conditions are treated by the chosen Eulerian EBM. Hence, the proposed solution of the boundary layer tracking problem can be described as an ALEEulerian formulation and implementation of an otherwise purely Eulerian EBM of interest. The basic features of this approach are illustrated with the Large Eddy Simulation on a non body-fitted mesh of a turbulent flow past an airfoil in heaving motion. Its potential for the simulation of challenging FSI problems at reasonable computational costs is also demonstrated with the computation of a turbulent flow past a highly flexible flapping wing.