Forthcoming networked systems require mechanisms for on-the-fly reconfiguration in their protocol stacks to be able to operate in different situations and networks. Since every protocol in a protocol stack has at least one peer protocol in another system, dynamic reconfiguration of a protocol raises the need for reconfiguration in the peer stack. For an assured dynamic (run-time) reconfiguration, executions of two peer protocols are stopped in a safe state, new protocols are initialized, and stacks switch to the new protocols at the same time. This paper proposes a software framework for dynamic reconfiguration of two communicating protocol stacks. A distributed algorithm is implemented in the framework of two communicating stacks in order to present an assured and synchronous reconfiguration of protocols. For demonstration, we have implemented a prototype of the framework and the algorithm to reconfigure two communicating TCP components by their secure version.