Transport and particulate processes are ubiquitous in environmental, industrial and biological applications, often involving complex geometries and porous media. In this work we present a general population balance model for particle transport at the pore-scale, including aggregation, breakage and surface deposition. The various terms in the equations are analysed with a dimensional analysis, including a novel collision-induced breakage mechanism, and split into one- and two-particles processes. While the first are linear processes, they might both depend on local flow properties (e.g. shear). This means that the upscaling (via volume averaging and homogenisation) to a macroscopic (Darcy-scale) description requires closures assumptions. We discuss this problem and derive an effective macroscopic term for the shear-induced events, such as breakage caused by shear forces on the transported particles. We focus on breakage events as prototype for linear shear-induced events and derive upscaled breakage frequencies in periodic geometries, starting from nonlinear power-law dependence on the local fluid shear rate. Results are presented for a two-dimensional channel flow and a three dimensional regular arrangement of spheres, for arbitrarily fast (mixing-limited) events. Implications for linearised shear-induced collisions are also discussed. This work lays the foundations of a new general framework for multiscale modelling of particulate flows.