Order picking is one of the most critical activities in the warehousing process. In order to obtain high profits, e-commerce retailers have focused on dedicated and accurate order picking methods. Zone picking is a picking approach commonly used for retail order picking where small-sized items have to be collected. Nevertheless, to become more efficient, it requires a scheduling policy for managing the bins flow which avoids blocking and mitigates order pickers unproductive times. This paper studies a specific variant of the Non-Permutation Flow-Shop (NPFS) scheduling problem with missing operations, transportation times and limited capacity constraints. A mathematical formulation of this new problem is proposed to minimize the total elapsed time for all machines. We study an illustrative example to analyze the differences between the optimal solution of the proposed model and a naive solution.