The chemical and dynamical processes in the upper atmosphere of Venus are poorly known. Recently obtained vertical profiles of trace species from the Venus Express mission, such as HCl, H2O, and HDO, provide new information to constrain these processes. Here, we simulate these profiles, using the model we have developed and described in a related paper by Yung et al. (2008), with special emphasis on the modeling of H2O and HDO. A new mechanism, the photo-induced isotopic fractionation effect (PHIFE) of H2O and HCl, is incorporated into our model. The observed enhancement of HDO could be attributed to (1) preferential destruction of H2O relative to HDO via PHIFE and (2) escape of hydrogen that enhances the abundance of D and hence its parent molecule HDO. Over a wide range of the sensitivity of the results to the changes of the two mechanisms, we find that the observed profiles of HDO and H2O profiles cannot be explained satisfactorily by current knowledge of chemical and dynamical processes in this region of the atmosphere. Several conjectures to tackle the problems are discussed.