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Various aspects of reliability modeling for systems that undergo changes in configuration during their mission are investigated in the context of Petri nets. In general, the duration of each phase for such multiphase scenarios can be either instantaneous (e.g., failure to activate on demand), deterministic (e.g., takeoff, cruise, and landing phases of a given aircraft mission), or random (e.g., time of spare activation, changes of stress levels due to component failure in shared-load systems). It is shown that utilizing recently introduced aging tokens provides a dynamic means for modeling complex multiphased missions without resorting to the use of marking dependence for generally distributed (nonexponential) failure distributions. Such a direct approach to the modeling of dynamically reconfigurable systems is contrasted with traditional methods previously described in the literature. Several examples are provided to illustrate the application of aging tokens to multiphase aging systems.