I have a python code to delete duplicate geometry..
code snippet:
gp.SelectLayerByAttribute_management(featureverticeshp_Layer, "NEW_SELECTION", gbgquery)
gp.SelectLayerByLocation_management(featureverticeshp_Layer, "ARE_IDENTICAL_TO", featureverticeshp_Layer, "", "NEW_SELECTION")
gp.SelectLayerByAttribute_management(featureverticeshp_Layer, "REMOVE_FROM_SELECTION", gbgquery)
gp.DeleteFeatures_management(featureverticeshp_Layer)
gp.SelectLayerByAttribute_management(featureverticeshp_Layer, "NEW_SELECTION", gbgquery)
gp.SelectLayerByLocation_management(featureverticeshp_Layer, "ARE_IDENTICAL_TO", featureverticeshp_Layer, "", "NEW_SELECTION")
gp.SelectLayerByAttribute_management(featureverticeshp_Layer, "REMOVE_FROM_SELECTION", gbgquery)
gp.DeleteFeatures_management(featureverticeshp_Layer)
If you want I can provide the entire code (author name: Gerry Gabrisch). (I forgot from where I download it, but works fine with shape file).