We present experimental and numerical results of the effect that a partial discharge has on the morphological and micro-mechanical properties of non-spherical, convex particles in a silo. The comparison of the particle orientation after filling the silo and its subsequent partial discharge reveals important shear-induced orientation, which affects stress propagation. For elongated particles, the flow induces an increase in the packing disorder which leads to a reduction of the vertical stress propagation developed during the deposit generated prior to the partial discharge. For square particles, the flow favors particle alignment with the lateral walls promoting a behavior opposite to the one of the elongated particles: vertical force transmission, parallel to gravity, is induced. Hence, for elongated particles the flow developed during the partial discharge of the silo leads to force saturation with depth whereas for squares the flow induces hindering of the force saturation observed during the silo filling.