Sorry I missed this post. In cases like this you can always create a new one referencing the old one. I had spoken to the R&D team on this. The issue here is because of an artifact of the visualization. There is only one data point for each layer in the simulation in the index data, placed at the position (along the propagation direction) in the middle of the layer. This means there is only one point for the substrate/cladding in the index data. The visualization then fills in half of the area between the substrate/cladding layer with the colors from the top/bottom layer in the visualization, creating this issue where the thicknesses looks different. I was told that the correct way to visualize the index data is to use view the transverse axes in the graph/visualizer. For example, if the propagation is z, then we should visualize the x and y axes. We should visualize the index in the xy plane, and the z-axis in the visualizer should be Slice. This means you view the xy plane for each value of z.
This artifact does not affect the results of your RCWA simulation.