Bana and Comon have proposed a logical approach to proving protocols in the computational model, which they call the Computationally Complete Symbolic Attacker (CCSA). The proof assistant Squirrel implements a verification technique that elaborates on this approach, building on a meta-logic over the CCSA base logic. In this paper, we show that this meta-logic can naturally be extended to handle protocols with mutable states (key updates, counters, etc.) and we extend \Squirrel's proof system to be able to express the complex proof arguments that are sometimes required for these protocols. Our theoretical contributions have been implemented in Squirrel and validated on a number of case studies, including a proof of the YubiKey and YubiHSM protocols.