The recently discovered structural reconstruction in the cuprate superlattice (SrCuO2)n/(SrTiO3)2 has been investigated across the critical value of n = 5 using resonant inelastic x-ray scattering (RIXS). We find that at the critical value of n, the cuprate layer remains largely in the bulk-like two-dimensional structure with a minority of Cu plaquettes being reconstructed. The partial reconstruction leads to quenching of the magnons starting at the Γ-point due to the minority plaquettes acting as scattering points. Although comparable in relative abundance, the doped charge impurities in electron-doped cuprate superconductors do not show this quenching of magnetic excitations.