Supervisory control reconfiguration has been paid more attention due to its capacity of handling the uncertainties including resource failures, capability degradation, and task changes in discrete event systems. However, the robustness of closed-loop systems in response to some specification changes was not addressed in the prior studies. This paper presents a reconfiguration method based on Petri nets and integer programming for supervisory control of resource allocation systems with changeable resource allocation relationships (control specifications). First, we propose a reconfiguration mechanism. It updates the P-invariant-based supervisor and evolves the state of the closed-loop system. The latter adapts to the certain changes in specifications by the self-regulation of the closed-loop system's state. It utilizes fully the robustness in a closed-loop system and avoids unnecessary modification of a supervisor. Then, a reconfiguration model with robustness analysis is proposed based on integer programming. By using it, a firing sequence of transitions as a serial of reconfiguration actions can be found. The execution of the sequence implements the state evolution of a closed-loop system. There is no need for making additional efforts to analyze state reachability of the system, since the firability condition of transitions is incorporated into the model. Finally, the method is illustrated through an example of a hospital emergency service system.