We propose a method for multilayer in-service reconfiguration for network computing systems that minimizes the total service downtime. Although both software and hardware virtualization technologies has been proposed for dynamic reconfiguration, each one is currently designed to be executed independently and thus their cooperative operations that dynamically reconfigure both of them have not been well-considered. We have developed a method for multilayer in-service reconfiguration that comprises Ethernet-based distributed device reconfiguration (hardware layer), fine-granular I/O service continuity management (software layer), and their orchestration. Application to the management of a session initiation protocol server system built on distributed resources demonstrated that this method achieves dynamic load balancing in response to call rate increases without any failed calls.