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We propose a controlled assembly Petri net with alternative route (CAPN-AR) model for a class of flexible assembly processes with alternative routes and unreliable resources. Alternative routes significantly enhance the reliability through the routing flexibility of the system. It is not required for a CAPN-AR to be live to maintain production. For this reason, we propose the concept of persistent production for the CAPN-AR. However, alternative routes also add complexity to the analysis of the systems. As the PNs grow rapidly with the scale of the problem, an existing reachability-tree method is feasible only for small nets. We propose an analysis method that can scale with the problems based on structural decomposition of the CAPN-AR. We study the conditions for persistent production, propose a deadlock avoidance algorithm with polynomial complexity for CAPN-AR, and access its robustness property with respect to resource failures.