The application of non-axisymmetric resonant magnetic perturbations (RMPs) to low current plasmas in the Mega Amp Spherical Tokamak (MAST) was found to be correlated with substantial drops in neutron production, suggesting a significant degradation of fast ion confinement. The effects of such perturbations on fast ions in MAST have been modelled using a revised version of a non-steady-state orbit-following Monte-Carlo code (NSS OFMC), in which the parametrization of fusion reaction rates has been updated and neutron rates have been recalculated. Losses of fast ions via charge-exchange (CX) with background neutrals and the subsequent reionization of fast neutrals due to collisions with bulk plasma particles have also been taken into account. The effects of the plasma response to externally-applied RMPs have been included in the modelling. The updated results show that computed neutron rates in the presence of RMPs with the plasma response and CX reactions taken into account agree very well with the experimental data throughout the analysis target time. CX reactions play an important role in determining the neutron rates, in particular before the onset of RMPs.