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Unreliable resources pose challenges in design of deadlock avoidance algorithms as resources failures have negative impacts on scheduled production activities and may bring the system to dead states or deadlocks. This paper focuses on the development of a suboptimal polynomial complexity deadlock avoidance algorithm that can operate in the presence of unreliable resources for assembly processes. We formulate a fault-tolerant deadlock avoidance controller synthesis problem for assembly processes based on controlled assembly Petri net (CAPN), a class of Petri nets (PNs) that can model such characteristics as multiple resources and subassembly parts requirement in assembly production processes. The proposed fault-tolerant deadlock avoidance algorithm consists of a nominal algorithm to avoid deadlocks for nominal system state and an exception handling algorithm to deal with resources failures. We analyze the fault-tolerant property of the nominal deadlock avoidance algorithm based on resource unavailability models. Resource unavailability is modeled as loss of tokens in nominal Petri Net models to model unavailability of resources in the course of time-consuming recovery procedures. We define three types of token loss to model 1) resource failures in a single operation, 2) resource failures in multiple operations of a production process and 3) resource failures in multiple operations of multiple production processes. For each type of token loss, we establish sufficient conditions that guarantee the liveness of a CAPN after some tokens are removed. An algorithm is proposed to conduct feasibility analysis by searching for recovery control sequences and to keep as many types of production processes as possible continue production so that the impacts on existing production activities can be reduced.