Problems restoring Windows 2000 Dual Boot-Up

This is my hardware configuration:

PIII 500 MHz
128 MB RAM
HDD 13.0 GB (Primary Master)
HDD 8.0 GB (Primary Slave)
SoundBlaster LIVE! 5.1
RIVA TNT2 Value 32 MB
56K Modem
IDE 48x CD-ROM (Secondary Master)
IDE 2x8x CD-R (Secondary Slave)
Realtek Ethernet Adapter

Operating Systems:
Windows 98 on C: (C:\WINDOWS)
Windows 2000 Professional on D: (D:\WINNT)

I installed Windows 98 first. And then Windows 2000 later. They were running fine until one day my brother inserted a Windows 98 boot floppy and from DOS mode typed:


This overwrote system files on drive C: I believe and the Dual-boot was gone. The computer would directly start to Windows 98. I think this has something to do with MSDOS.SYS and IO.SYS files. Of course, the Windows 2000 folders were all intact on drive D but the C:\ root got disturbed by doing SYS C:

Someone told me to repair my Windows 2000 installation. I inserted the Windows 2000 Professional CD and restarted my PC. There I got the option of "REPAIR A WINDOWS 2000 INSTALLATION". I did that. It did some repairs and restarted again. But no use. It still started directly in Windows 98 and there was no Dual-Boot menu.

What I did now was, I restarted my PC again with the Windows 2000 Professional CD and went on to setup. Now, this time, I chose the option "CLEAN INSTALL" instead of "REPAIR ... " Thinking that this might help, I proceeded. It asked me the drive and folder I would like to install Windows 2000 to. I gave the same D:\WINNT folder. It came up with a message that this folder will be overwritten and the all the user accounts will go. Well, there seemed to be no other way !!! It installed Windows 2000 Professional again and of course worked fine this time. There was a dual-boot menu. But all the user accounts / programs went away.

Now my question is: Is there a way to repair a Windows 2000 installation / dual-boot ?? Why doesn't the repair option that comes when you run the setup work fine ?? Was there something wrong I did ? Does this mean that everytime I re-install Windows 9X, I will have to re-install Windows 2000 again ??? I'd be really grateful if someone can give me the answers as I'm planning to re-install Windows 98 again but I DO NOT want to lose Windows 2000 accounts / programs. I just want to install Windows 98 WITHOUT disturbing the Windows 2000 installation.
Who is Participating?
When you have Win98 installed and you install W2K the installation process of W2K is making a backup of your current W98 bootsector in a file called 'C:\bootsect.dos'.
Via this file the W2K bootmenu is able to start W98.
What 'SYS C:' is doing is replacing the W2K bootsector with a new W98 bootsector.
(The bootsector contains information which files to use for startup.)
You could have solved this by starting up with the W2K installation cd-rom and choosing the Command Recovery Console.
In this console you can replace the original W2K bootsector.
After this everything should be OK again.

Now you re-installed W2K and hopefully you didn't do anything with the W98 installation. Then you can try and check if the file c:\bootsect.dos is still available on your hard drive.

Start a dosprompt via 'Start | Run | cmd <enter>
type: c: | cd\ | dir/a bootsect.dos
If you see this file then this file contains the bootsector of W98.
If the file exist you can try this.
type: attrib boot.ini -s -h -r | copy boot.ini
      edit boot.ini
You're now in the editor
Add the following line at the end of boot.ini
     c:\bootsect.dos="Windows 98"

Reboot your PC and in the selection menu choose for "Windows 98".
Hope this helps.

Lee W, MVPTechnology and Business Process AdvisorCommented:
To elaborate on what hendrik999 says, you go into the recovery console using the Windows 2000 CD or setup floppys (choose repair as initial option).  This will load a DOS-prompt-like window, which will require your administrator password to login.  Then you can use the "Fixboot" command which "Writes a new partition boot sector onto the system partition".  "Fixmbr" may also come in handy at times as it "Repairs the master boot record of the partition boot sector" (Info from Pages 520 & 521 of the MCSE Training Kit for Windows 2000 Professional)

Another thing you could have done was installed Windows 2000 to "d:\winnt.tmp" (or some other directory instead of your original Win2K installation) and this would have restored the boot record.  Once restored, you could go into the second listing for Windows 2000 in the boot menu (which should be your original installation) and just delete the new one in "d:\winnt.tmp".  You would then also have to edit the c:\boot.ini file so that it only gave one option to boot into Win2k.
ki007Author Commented:
Thanks guys!!! I'll go and give it a try.

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