Many classical synchronization problems such as the assembly line crew scheduling problem (ALCS), some data association problems or multisensor tracking problems can be formulated as finding intra-column rearrangements for a single matrix representing costs, distances, similarities or time requirements. In this paper, we consider an extension of these problems to the case of multiple matrices, reflecting various possible instances (scenarios). To approximate optimal rearrangements, we introduce the Block Swapping Algorithm (BSA) and a further customization of it that we call the customized Block Swapping Algorithm (Cust BSA). A numerical study shows that the two algorithms we propose -in particular Cust BSA -yield high-quality solutions and also deal efficiently with high-dimensional set-ups.