Networks on Chip (NoC) have emerged as the design paradigm for scalable System on Chip (SoC) communication infrastructure. Due to convergence, a growing number of applications are integrated on the same chip. When combined, these applications result in use-cases with different communication requirements. The NoC is configured per use-case and traditionally all running applications are disrupted during use-case transitions, even those continuing operation.In this paper we present a model that enables partial reconfiguration of NoCs and a mapping algorithm that uses the model to map multiple applications onto a NoC with undisrupted Quality-of-Service during reconfiguration. The performance of the methodology is verified by comparison with existing solutions for several SoC designs. We apply the algorithm to a mobile phone SoC with telecom, multimedia and gaming applications, reducing NoC area by more than 17% and power consumption by 50% compared to a state-of-the-art approach.