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Internet of Things (IoT) technologies enable development of reconfigurable manufacturing systems–a new generation of modularized industrial equipment suitable for highly customized manufacturing. Sequential control in these systems is largely based on discrete events, whereas their formal execution semantics is specified as control interpreted Petri nets (CIPN). Despite industry-wide use of programming languages based on the CIPN formalism, formal verification of such control applications in the presence of adversarial activity is not supported. Consequently, in this article, we introduce security-aware modeling and verification techniques for CIPN-based sequential control applications. Specifically, we show how CIPN models of networked industrial IoT controllers can be transformed into time Petri net (TPN)-based models and composed with plant and security-aware channel models in order to enable system-level verification of safety properties in the presence of network-based attacks. Additionally, we introduce realistic channel-specific attack models that capture adversarial behavior using nondeterminism. Moreover, we show how verification results can be utilized to introduce security patches and facilitate design of attack detectors that improve system resiliency and enable satisfaction of critical safety properties. Finally, we evaluate our framework on an industrial case study.