Hi Duncan,
The Home, Temp, and Workspace locations saved in the AGWA Preferences are stored in the XML file associated with MXD map document (it is in the same location with the same name as the map document with the addition of a .xml extension). This is why the map document must be saved before AGWA allows you to save your preferences, because the XML file can't be created until the map document is saved. If you use Windows Explorer to copy, move, rename, or delete a map document, the same will not be done to the associated XML document because Windows doesn't recognize the connection between the .mxd document and the .mxd.xml file. Consequently, the saved preferences will be lost in the file that is copied, moved, or renamed. However, If you do any of these operations using ArcCatalog or the Catalog window in ArcMap then the saved preferences will persist in the copied, moved, or renamed map document. Also note that because of this, the Home, Temp, and Workspace preferences must be set for each map document used with AGWA.
Thanks for your suggestion to add this information to the documentation. I will make sure it's there next time the documentation is updated.
Shea