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When opening a .mxd in ArcGIS/ArcMap that had a WaterGEMS model attached, the model is no longer associated. If the model is added to the .mxd again, then duplicate layers are created.This behavior is common when the files are moved to a new location.
Note: This behavior applies to using WaterGEMS, SewerGEMS and HAMMER models in ArcGIS/ArcMap, but for simplicity this article will reference WaterGEMS.
Basically ArcGIS has historically stored the "absolute" path to data sources in the .mxd. Meaning, when you open a .mxd file, it looks for all the associated layers in the exact original path that they were saved in. This applies to other layers you may have added, not just WaterGEMS layers. So, if you move the .mxd file, WaterGEMS model files, geodatabase, and other layers you had to a new location and try to open it, it won't be able to load any of those layers, because they're referring to the old path. This is why you see red exclamation points next to all the layers in the table of contents. In short, the problems you're having with moving projects are due to ArcGIS limitations, which WaterGEMS has no control over. With that being said, recent versions of ArcGIS have added the ability to use the "relative" path. This way, it will look for the other data sources in the same folder as the .mxd file. In ArcGIS 9.3.1, this option is under File > Document Properties > Data Source Options. In ArcGIS version 10.X, this is under File > Map Document Properties > "store relative pathnames to data sources". So, you would simply need to have this option checked before moving the files to the new location.
Here is the full workflow for moving a WaterGEMS for ArcGIS project from one location to another:
1. On the old location/computer, open the .mxd file associated with the WaterGEMS model2. Go to File > Document Properties and make sure the option to use relative paths is selected.3. Save the .mxd file and close ArcGIS4. Move the .mxd, .wtg, .wtg.sqlite, .mdb and any other data sources/layers to the new location/computer5. Open the .mxd file file on the new computer - it should automatically see the data sources in the same folder as the .mxd and load them. Symbology changes should be retained.
WaterGEMS For ArcGIS [FAQ]