In this paper we study the behavior of the Casimir energy of a multi-cavity across the transition from the metallic to the superconducting phase of the constituting plates. Our analysis is carried out in the framework of the ARCHIMEDES experiment, aiming at measuring the interaction of the electromagnetic vacuum energy with a gravitational field. For this purpose it is foreseen to modulate the Casimir energy of a layered structure composing a multi-cavity coupled system by inducing a transition from the metallic to the superconducting phase. This implies a thorough study of the behavior of the cavity, where normal metallic layers are alternated with superconducting layers, across the transition. Our study finds that, because of the coupling between the cavities, mainly mediated by the transverse magnetic modes of the radiation field, the variation of energy across the transition can be very large.