Multi-reference calculations along the lines of the Generator Coordinate Method or the restoration of broken symmetries within the nuclear Energy Density Functional (EDF) framework are becoming a standard tool in nuclear structure physics. These calculations rely on the extension of a single-reference energy functional, of the Gogny or the Skyrme types, to non-diagonal energy kernels. There is no rigorous constructive framework for this extension so far. The commonly accepted way proceeds by formal analogy with the expressions obtained when applying the generalized Wick theorem to the non-diagonal matrix element of a Hamilton operator between two product states. It is pointed out that this procedure is ill-defined when extended to EDF calculations as the generalized Wick theorem is taken outside of its range of applicability. In particular, such a procedure is responsible for the appearance of spurious divergences and steps in multi-reference EDF energies, as was recently observed in calculations restoring particle number or angular momentum. In the present work, we give a formal analysis of the origin of this problem for calculations with and without pairing, i.e. constructing the density matrices from either Slater determinants or quasi-particle vacua. We propose a correction to energy kernels that removes the divergences and steps, and which is applicable to calculations based on any symmetry restoration or generator coordinate. The method is formally illustrated for particle number restoration and is specified to configuration mixing calculations based on Slater determinants.
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