Directly in the file system. I overwrote the old file as part of the GIS processing. My mistaken assumption was that the initial conditions are for each run are read in from the file that was used when creating the initial condition portion of a scenario. I now know that is not the case. I am sure it was explained in the training and I have just forgotten. Thanks for being patient as I work through understanding the interface and how to run the software in a iterative development mode.