This is a collection of actions I've learned to take when I'm having problems with ArcHydro or HEC-GeoHMS. I'll add to the list when I find more.
- Make sure the Geoprocessing extents include the whole project: Go to the Geoprocessing menu>Environments...>Processing Extent. Under Processing Extent choose a layer that you know covers the full extent of the waters you are processing and click OK. This should ensure that the processing extent is large enough to do what you want.
- Delete everything you can in your temp folder: Mine is C:\Users\mboucher\AppData\Local\Temp. Get out of ArcMap first to clear temp files related to your project. You can do this without getting out of ArcMap through the ArcHydro Toolbar under ApUtilities>Additional Utilities>Clean User's Temp Folder.
- Make sure your Target Locations are correct: Under ApUtilities>Set Target Locations, make sure the HydroConfig and they GeoHMSConfig Targets make sense. The raster data should go to the project folder vector data to a geodatabase. The raster data will go to a folder in the project folder with the dataframe name and the vector data to a feature data set with the dataframe name. Through the ArcHydro Toolbar under there is a function to reset the target locations: ApUtilities>Additional Utilities>Reset Target Locations. I've not tested this to see if it corrects everything.
- When working on a complicated model, don't use the model mxd for your presentation map. It just adds baggage to an already "heavy" mxd.