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This paper focuses on reconfiguration aspects of agent-based industrial control systems. Reconfiguration is the ability of the control system to modify its behavior to cope with unusual conditions and changes of the production environment like machine breakdowns, product innovations, rush orders, etc. This paper presents a multiagent system dedicated to material flow control-manufacturing agent simulation tool (MAST)-and discusses in detail how agents efficiently cope with the dynamic reconfiguration. Two scenarios are discussed: 1) the automatic reconfiguration of the transportation paths carried out by agents in case of failures and 2) the structural reconfiguration enabling online addition, removal, or reconnection of equipment or transportation paths on the factory floor. Two proof-of-concept applications of MAST in University of Cambridge's and Vienna University of Technology's testbeds are described.