For the calculation of core-ionization energies (IE), X-ray photoelectron spectroscopy (XPS), and X-ray emission spectroscopy (XES), a commonly applied approach is to use non-Aufbau reference states with a core-hole as either final (IE and XPS) or initial (XES) state. However, such reference states can introduce numerical instabilities for post-HF methods, relating to the denominator of the energy corrections involved. This may become arbitrarily close to zero if a negative virtual MO is present, e.g. a core-hole, leading to near-singularities. The resulting instabilities lead to severe convergence issues of the calculation schemes and, in addition, can strongly affect both energies and intensities, with oscillator strengths seen to reach values up to 4 × 10^7. For the K-edge we propose freezing the highest-energy virtuals which contribute to any denominator below a threshold of 0.1 Hartree. Stable and reliable spectra are then produced, with minimal influence due to freezing energetically high-lying virtuals (typically removing <5% of the total number of MOs). The developed protocol is here tested for Møller–Plesset perturbation theory and for the algebraic diagrammatic construction scheme for the polarization propagator, but it is also relevant for coupled cluster theory and other related methods.