My limited experience with Explorer configuration files in build 1500 is that once a configuration is set, it is used in every Explorer document on that machine. I would prefer if I could set different configurations for different documents.
Currently, when I share a configuration file with a user (we'll call it Config A), they open it, add a few notes or whatever and save it out to a new Explorer map. This new map is still based on the default configuration despite the fact it was saved from a document referencing Config A. They have now lost all customizations and have to redirect the map to Config A to get them back. However, once they've done that they can no longer open a vanilla version of ArcGIS Explorer unless they remove the configuration reference and set it back to default. It's a confusing mess.
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