The design of the protection system for the superconducting portion of the 45-T Hybrid Magnet System being constructed at the National High Magnetic Field Laboratory and the establishment of safe and reliable operating procedures are critical tasks. To support these efforts, the finite element code SARUMAN has been extended to include capability for analysis of the stability and quench in Cable-in-Conduit Conductors (CICC) cooled by pressurized superfluid He II. This modification consists of introducing a temperature gradient term in the energy equation for the counterflow mechanism and extension of the properties of helium and other materials of the magnet to the He II temperature region. Using this new version of the code, the stability of the conductors for the 45-T Hybrid have been analyzed against different thermal disturbances and under a variety of possible operating conditions, as well as the evolution of the quench in the conductor.