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Automated Manufacturing Systems (AMSs) can process different parts according to operation sequences sharing a finite number of resources. In these systems deadlock situations can occur so that the flow of parts is permanently inhibited and the processing of jobs is partially or completely blocked. This paper proposes a control strategy to manage resources in complex systems where multiple resource acquisitions are allowed to complete a working operation (Conjunctive Resource Service System-CRSS). The AMS structure and dynamics is described by a Colored Timed Petri net model, suitable for following resource changes and working procedure updating. Moreover, on the basis of the deadlock characterization obtained by digraph tools, an event-based controller is defined to avoid deadlock in CRSSs.