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I manually edited an ArcXML file to include elements not available in Author, such as additional symbology, query statements, or map projections. When I open that ArcXML file in ArcIMS Author or ArcExplorer—Java edition and open the Layer Properties dialog, the changes don't display.
Once you make edits of this nature, you should not attempt to save the map
configuration file in ArcIMS Author. ArcIMS Author does not recognize the additional elements and they are lost.
You can use the modified ArcXML file in ArcIMS Designer or ArcIMS Administrator like any other map configuration file, just don't save it in ArcIMS Author or ArcExplorer—Java edition as it will cause the manual edits to be removed.