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In many flexible assembly systems, base components are transported with pallets; parts to be mounted onto the base ones are transported by trays with no pallets. When an assembly operation is performed by using some parts in a tray but not all, the tray with the remaining parts still occupies a buffer space. In this way, an assembly/disassembly material flow is formed. In such a material flow, deadlock can occur both in the base component and part flow. Furthermore, the assembly operations can also result in a deadlock. Thus, it is a great challenge to tackle deadlocks in such processes. This paper models them using resource-oriented Petri nets. Based on the models, a deadlock control policy is proposed and proved to be computationally efficient and less conservative than the existing policies in the literature. An industrial case study is used to show the results.