When doing my Wx grids, I typically will run Step 6 in 12-hour blocks as I go through and evaluate the PoP/Thunder grids. I have noticed using this method, when it goes through and reruns the Hazard Builder grids, that the HBFlooding grid is only recalculated during the nighttime periods. If I rerun Step 6 using a 24-hour block of 00Z-00Z, then the daytime HBFlooding grid will be recalculated as well. I've attached an example of a 24-hour period which had Step 6 run in two 12-hour blocks.
