Why shouldn I use ArcIMS 3.0 shapefile spatial indexes with ArcIMS 3.1?
ArcIMS 3.1 offers faster spatial indexes for shapefiles. In addition, bugs with spatial indexes for shapefiles were fixed at ArcIMS 3.1. If you have any problems displaying a shapefile, deleting the spatial index may solve the problem. Shapefile spatial indexes that were built with ArcIMS 3.0 should be deleted and rebuilt with ArcIMS 3.1. To do this, delete the shapefile .sbn and .sbx files. When you publish a MapService that uses the shapefile, the ArcIMS Spatial Server will generate new spatial index files.