A model of a free electron laser (FEL) operating with an elliptically polarised undulator is presented. The equations describing the FEL interaction, including resonant harmonic radiation fields, are averaged over an undulator period and generate a generalised Bessel function scaling factor, similar to that of planar undulator FEL theory. Comparison between simulations of the averaged model with those of an unaveraged model show very good agreement in the linear regime. Two unexpected results were found. Firstly, an increased coupling to harmonics for elliptical rather than planar polarisarised undulators. Secondly, and thought to be unrelated to the undulator polarisation, a significantly different evolution between the averaged and unaveraged simulations of the harmonic radiation evolution approaching FEL saturation.