A multi-unit resource allocation system usually contains several processes and a number of resources with multiple units. Due to the competition for shared resources in these systems, deadlocks may occur. Recently, researchers have shown an increased awareness in deadlock control strategies for such a kind of systems without considering the dynamic changes such as processing failures and rework by using the Petri net paradigm. This article reports a new strategy for deadlock analysis and control in reconfigurable multi-unit resource systems (MRSs). We discuss a generalized class of Petri nets in which each stage of a process may require a number of units of different types of resources to perform a task. In this way, we can model more complex real systems. Thanks to a generalized class of Petri nets, i.e., the system of sequential systems with shared resources (S4R), this article proposes an effective integrated strategy for designing robust supervisors for reconfigurable MRSs, and improves an S4R model to achieve a new model, namely a system of sequential systems with shared resources and part-re-entry (S4RP), which represents the procedure that a flawed product re-enters a system and is re-processed. We use a siphon-based max-controllability deadlock prevention policy (DPP) to supervise the evolution of the S4RP, and present a comprehensive analysis to demonstrate that the controlled S4RP is free of deadlocks. A net analysis tool (INA) is used to test and validate the resulting S4RP.