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When attempting to recalculate or change the spatial index for a feature class with archiving enabled, the command can fail when attempting to change the archive feature class from load_only mode to normal_io mode.
The cause of the problem is that the process that moves a SDEBINARY layer from load_only mode to normal_io mode does not detect that the layer being modified is an archive feature class. The process attempts to place a unique index on the archive class shape attribute, which fails if any features have been archived since archiving was initialized (because of duplicate shape values).
The problem is specific to archive classes stored as SDEBINARY. If using ArcGIS 9.3, one option is to use the Geoprocessing Tool migrate storage to convert the feature class and archiving class from SDEBINARY to st_geometry. If this is not a feasible solution or ArcGIS 9.2 is being used, please contact ESRI Technical Support.