Flow-fields are typically used to intimately mix large μm-sized particles with polymer melts. Here we show, using rheology, X-ray scattering, and electron microscopy, that shear flows do not improve the spatial dispersion or ordering of spherical nanoparticles (NP) grafted with polymer chains over the ranges of flow fields realizable in our experiments in the melt state. In the absence of flow, grafted NPs robustly self-assemble into a variety of superstructures when they are added to a homopolymer matrix with the same chemistry as the NP grafts. We find that isolated particles and spherical NP clusters remain dispersed but do not flow align. On the other hand, anisotropic NP assemblies initially break and their constituent building blocks (strings or sheets) flow-align locally. At very large strains, they coarsen into large aggregates, reflecting the dominance of interparticle attractions over flow fields and thermal energy.