Why is there a difference between the Rfactors from Refmac and Sfcheck?
Sfcheck usually does not have enough information to reproduce your full refinement. In particular, it does not reproduce the solvent model, TLS refinement, anomalous terms, variant scattering factors, etc. So it cannot reproduce your original Fcalc values. Given that it has different Fcalc, it is no wonder that it also has different R values.