If problems are occurring due to management becoming confused (e.g., when deleting or renaming water supplies or Control Valves) access Design|Clear Management and then Assign Zones to System Flows tools to reset the management.
In versions older than V10 delete the .wsp file (system flows designated to water supplies) or the .stn file (zones operating on system flows). These files will be found where you have saved the design, commonly C:\Program Files\AEI Software\Irricad Pro 10\Design.