Cloud applications are complex applications composed of a set of interconnected software components running on different virtual machines, hosted on remote physical servers. Deploying and reconfiguring this kind of applications are very complicated tasks especially when one or multiple virtual machines fail when achieving these tasks. Hence, there is a need for protocols that can dynamically reconfigure and manage running distributed applications. In this article, we present a novel protocol, which aims at reconfiguring cloud applications. This protocol is able to ensure communication between virtual machines and resolve dependencies by exchanging messages, (dis)connecting, and starting/stopping components in a specific order. The interaction between machines is assured via a publish-subscribe messaging system. Each machine reconfigures itself in a decentralized way. The protocol supports virtual machine failures, and the reconfiguration always terminates successfully even in the presence of a finite number of failures. Due to the high degree of parallelism inherent to these applications, the protocol was specified using the LNT value-passing process algebra and verified using the model checking tools available in the CADP toolbox. The use of formal specification languages and tools helped to detect several bugs and to improve the protocol.