We study shear flow in liquid crystal cells with elastic deformations using a lattice Boltzmann scheme that solves the full, three-dimensional Beris-Edwards equations of hydrodynamics. We consider first twisted and hybrid aligned nematic cells, in which the deformation is imposed by conflicting anchoring at the boundaries. We find that backflow renders the velocity profile non Newtonian, and that the director profile divides into two regions characterized by different director orientations. We next consider a cholesteric liquid crystal, in which a twist deformation is naturally present. We confirm the presence of secondary flow for small shear rates, and are able to follow the dynamical pathway of shear-induced unwinding, for higher shear rates. Finally, we analyze how the coupling between shear and elastic deformation can affect shear banding in an initially isotropic phase. We find that for a nematic liquid crystal, elastic distortions may cause an asymmetry in the dynamics of band formation, whereas for a cholesteric, shear can induce twist in an initially isotropic sample. (C) 2004 American Institute of Physics.