On an FDTD simulation you don't really change things in time since the transient time of any of the optical phenomena, specially transmission through a medium, is much shorter than anything you would simulate to be changing. So you probably are thinking of running several simulations, each with a change in the refractive index, and grouped in a compact model to simulate that transient response in the circuit simulator (Interconnect). 

You can follow any of the Active examples that guide you on how to do the complete process. Like this one: