Recently, a computational technique for ab initio calculation of the inter-atomic and intermolecular non-radiative decay processes has been developed [1]. It combines the Fano formalism with the Green's function method known as the algebraic diagrammatic construction. The problem of normalization of continuum wave functions stemming from the use of the Gaussian basis sets is solved by using the Stieltjes imaging technique. In the present paper, the methodology is extended in order to describe the inter-atomic decay of excited doubly ionized states of clusters. The new computational scheme is applied to compute the inter-atomic decay rates of doubly ionized states formed by Auger relaxation of core vacancies in NeAr and MgNe van der Waals clusters.