For a NetWare server, follow the instructions in the GroupWise Installation Guide for your version of GroupWise:
GroupWise 2012: N/A.
GroupWise 8: Uninstalling the NetWare GroupWise Agents
Be sure to remove the migrated agents from the NetWare autoexec.ncf file so that the server does not try to start the migrated agents automatically when it is restarted.