Thin film solar cells based upon CdS-CdTe heterojunctions have become an important alternative to silicon based devices. The film structures formed during fabrication are critical to cell efficiency and thus their study is fundamental to improving device performance. We have used synchrotron x-ray diffraction to investigate the effect of a post deposition anneal upon the film structures and, in particular, have examined the dynamic formation of intermixed regions adjacent to the original, metallurgical interface. Our results have enabled us to produce a dynamic model for the structural changes which includes the extent of interdiffusion. We show that, for a 400 nm CdTe film in the presence of chlorine, the original CdS and CdTe layers are completely transformed into layers with average compositions CdS0.93Te0.07 and CdTe0.94S0.06, respectively. We present evidence that the interdiffusion occurs during or following a recrystallization and that, to a limited extent, these changes also occur without chlorine.