I don't think you will be required to change the material of your FDTD simulation based on the CHARGE simulation. In a photodiode, optical energy is converted to electrical energy. So, we first perform the FDTD simulation to calculate the absorption and generation rate in a material when light is incident on it. We export these results to CHARGE to perform the electrical simulation and determine results such as the photocurrent. An example of the approach can be found on the following page: Vertical photodetector.
What you mention here is relevant for other applications such as PIN modulator. The operation of a PIN modulator is based on change in refractive index of a material due to charge injection. In these cases, you can use the np density Index Perturbation to account for the index perturbation of the material from the carrier density. An example is shown here: PIN Mach-Zehnder modulator.