The assembly of nematic colloids relies on long-range elastic interactions that can be manipulated through external stimuli. Confinement and the presence of a hydrodynamic field alter the defect structures and the energetic interactions between the particles. In this work, the assembly landscape of nanoparticles embedded in a nematic liquid crystal confined in a nanochannel under a pressure-driven flow is determined. The dynamics of the liquid crystal tensor alignment field is determined through a Poisson-Bracket framework, namely the Stark-Lubensky equations, coupled with the zero-Reynolds momentum equations and the liquid crystal Landau-de Gennes free energy functional. A second order semi-implicit time integration and a three-dimensional Galerkin finite element method are used to resolve flow and nematic fields under several conditions. In general, the zero Reynolds flow displaces the defects around the particles in the upstream direction and renders the surface anchoring ineffective when the flow strength dominates over the nematic elasticity. More importantly, the potential of mean force for particle assembly is non-monotonic independent of surface anchoring. Our results show that the confinement length scale determines the repulsion/attraction transition between colloids, while the flow strength modifies the static defect structure surrounding the particles and determines the magnitude of the energetic barrier for successful assembly. In the attractive regime, the particles move at different rates through the nematic until one particle eventually catches up with the other. This process occurs against or along the direction of flow depending on the flow strength. Ultimately, these results provide a template for engineering and controlling the transport and assembly of nanoparticles under far-from equilibrium conditions in anisotropic media.