If an integrated Windows server becomes damaged, you may be able to preserve installed applications and user data by reinstalling it. Try either logging on or starting up with DOS by using the Boot menu of the NT loader (NTLDR). (This is only possible if the boot drive is still formatted as FAT.) You can then reinstall Windows server. Doing this returns the system to the base level code of Windows server originally installed. You must then reapply any Microsoft service packs that you had installed. You should also reinstall the latest IBM iSeries Integrated Server Support service pack.
To reinstall Windows server, try this.
D: cd \i386 winnt /s:D:\i386 /u:D:\unattend.txt
Windows 2000 Server and Windows Server 2003 also provide the Windows Recovery Console, which is a command-line console that provides limited access to the system to perform many administrative tasks or repair the system. Refer to the Windows 2000 Server or Windows Server 2003 documentation for additional information.
You may also have to reinstall from the very beginning by following this procedure: Start the installation from the i5/OS console.