In this study, it was evaluated whether the whey protein nitrogen index (WPNI) of a range of skim milk powder (SMP) samples was correlated with the heat stability of the corresponding recombined filled evaporated milk (RFEM), as well as with the extent of lactosylation and changes in whey proteins (WPs). Pulsed field gradient NMR results showed that the diffusion coefficients of lactose in all samples varied only to a small extent, while the diffusion coefficients of the WP fraction ranged more widely. A lower heat stability of RFEM produced from SMP with a lower WPNI was found as compared with those with a higher WPNI: principal component analysis (PCA) and correlation analysis revealed that the decreased heat stability could be at least partly explained by the increased calcium solubilization induced by the lower pH of dispersions of SMP with a lower WPNI. Although it was claimed over the years that high-heat SMP (with a low WPNI) is beneficial to ensure a better heat stability of RFEM, it is clear from our results that a low WPNI of SMP alone was not sufficient to guarantee a better RFEM-heat stabilizing functionality.