Co-based full Heusler alloys have attracted significant attention due to their high spin polarisation and successful integration as electrodes in magnetic tunnelling junctions and current-perpendicular-to-plane spin valves (CPP-SV). Further improvement of the CFMS based CPP-SVs requires a fundamental understanding of the effects of atomic disorder within the Heusler alloys. In this work we present a theoretical study of disorder in CFMS alloys using ab initio simulations, guided by images from Z-contrast scanning-TEM of sample films. The simulations are based on density functional theory plus a Hubbard U term, allowing the investigation of the effects of atomic disorder on the spin-polarisation at the Fermi level, and computation of the disorder formation energy. It is found that in order to retain the high spin-polarisation at the Fermi level the integrity of the Co-sublattice should be preserved, but that the effect of mixing between the Fe/Mn and Si sublattices (B2 phase) varies dramatically depending on the precise nature of the disorder and the chemical composition of the CFMS. Calculations of the spin-polarisation at the Fermi energy show that Co2Fe0.5Mn0.5Si is especially robust with respect to such intermixing, an observation which may explain the good performance of films in this composition range.