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In reconfigurable manufacturing systems (RMSs), the architecture of a system can be modified during its operation. This reconfiguration can be caused by many motivations: processing rework and failures, adding new products, adding new machines, etc. In RMSs, sharing of resources may lead to deadlocks, and some operations can therefore remain incomplete. The objective of this article is to develop a novel two-step solution for quick and accurate reconfiguration of supervisory controllers for deadlock control in RMSs with dynamic changes. In the first step, the net rewriting system (NRS) is used to design a reconfigurable Petri net model under dynamic configurations. The obtained model guarantees boundedness behavioral property but may lose the other properties of a Petri net model (i.e., liveness and reversibility). The second step develops an automatic deadlock prevention policy for the reconfigurable Petri net using the siphon control method based on a place invariant to solve the deadlock problem with dynamic structure changes in RMSs and achieve liveness and reversibility behavioral properties for the system. The proposed approach is tested using examples in the literature and the results highlight the ability of the automatic deadlock prevention policy to adapt to RMSs configuration changes.