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Reinstall a Dual-Booted Windows 9x/Me

Last reviewed: March 2004

How to reinstall a Windows Me, SE, 98, or 95 dual-booted with a Windows XP, 2000, or NT, and still retain the dual-boot.

Reinstalling a dual-booted Windows 9x is usually easy.
These reinstalls apply only to when Windows 9x/Me is installed on C: (PC system partition) and XP/2K/NT is on another partition. You will be able to adjust this information to fit your own circumstances. If using a third-party boot manager, you must refer to its own Readme file for instructions.

Three methods of reinstalling Win9x are described here. The Overlay method is "too easy" but can work! The Delete method will be favoured by, and work for, many users. The Format method produces a fresh and clean system, and is essential in serious degradation or if a virus is suspected.

There's never a total guarantee that all systems will follow the normal pattern. Therefore it's strongly recommended that all users protect themselves with a new Rescue Boot Disk and a backup of important data first. If your problem is with the dual-boot itself, you should go to Repair a Dual-Boot.

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NEVER Dual-Boot without your personal safety net - a BOOT DISK
If stuck, use a Win9x Startup Disk (CD support), and run WINNT.EXE from I386 folder on CD.

RESCUE BOOT DISK for when XP, 2K, NT will not boot - ESSENTIAL, 1 floppy
   Create this floppy yourself to get XP, 2K, NT running even if the boot record,
   or boot files, are ever a problem. Write-protect and keep it safe.
      Format a floppy with that XP, 2K, or NT. It must be a full XP/2K/NT format.
      Alter file Attributes (Attrib -r -s -h) of these files in root of C: (PC system partition)
      Boot.ini, NTLDR,, and Bootsect.dos & Ntbootdd.sys (if present)
      (plus Arcldr.exe & Arcsetup.exe - for Windows 2K) and copy them to the floppy.
      Write-protect the floppy. Then restore original Attributes to the files on C:.
      Read the Rescue Boot Disk page for full details, plus a much improved Rescue disk.

The huge benefit of this boot disk is that you can still run your Windows XP/2K/NT even if there is a problem with the boot files or with the boot sector - those are run from the floppy. The Windows XP, 2000, NT itself will run from its own OS boot partition.

A further benefit is that the Rescue Boot Disk is a backup for all the boot files. These include the important Boot.ini (the boot initialization file), and NTLDR (the boot loader), plus Bootsect.dos (a copy of the Win9x boot sector), and others.

The Rescue Boot Disk page also shows how to add extra lines to A:\Boot.ini so your XP/2K/NT will still boot even if there is confusion (Windows, or user!) about the boot path for the XP/2K/NT line(s) in Boot.ini. It is known that the default line in Boot.ini can, on occasions, be incorrect.

A Rescue Boot Disk is obligatory in all dual-boots, indeed for all XP/2K/NT users.


The XP/2K/NT boot sector has control of this dual-boot.

Please note that some Win9xs seem more aware than others of the existence of another OS. Also, its been reported that some Win9x installations remove boot files for XP/2K/NT, while others do not and do not even interfere with the established dual-boot.

The following actions will definitely break the XP/2K/NT boot sector:
1. Using SYS C:, or FDISK /MBR, from the Win9x boot disk.
2. Format of the C: drive.
Fortunately, the XP/2K/NT boot sector & the dual-boot can be repaired.

Win9x Reinstall Options:

(a). Overlay Reinstall - Not clean.
This is the least preferable option. Win9x is simply installed over itself.
The dual-boot will be retained. This can clear problematic Win9x files.

(b). Delete Win9x + other files & Reinstall - Windows clean.
This is likely to be the most popular option. The dual-boot should be retained.
This will clear problematic Win9x, & other, files.

(c). Format C: & Reinstall - Fully clean (Partition & Boot Sector)
This is the most thorough option and is also suitable for a possible virus.
It requires greater user participation and some attention to detail.

Run a full Thorough/Surface Scandisk on C: before a Win9x reinstall.

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Reinstall Windows 9x over the existing Windows 9x.

At first sight this is simple. Do the minimum. Don't format and delete little.
Just install the Win9x over the existing Win9x installation!
Settings, software, passwords, e-mails, etc., and drivers should remain intact.

1.   Make sure your Win9x boot disk gives CD access, or copy its files/Cabs to hard disk.
2.1 Boot to XP/2K/NT and create the Rescue Boot Disk.
2.2 Make Win9x the Default boot option.
2.3 Rename the Win9x files WIN.COM, VMM32.VXD, perhaps others (not the Registry!).
3.   Boot the Win9x boot disk to true DOS and reinstall Win9x over the existing Win9x.
      You can use   setup /is
      Do not alter the file system (FAT or FAT32) used by C:.

The dual-boot will, or should, be retained.
If not, copy these boot files from the recently created Rescue Boot Disk to C:\
Boot.ini, Ntldr,, Bootsect.dos, (maybe Ntbootdd.sys, Arcldr.exe, and Arcsetup.exe).
(if necessary, use fixboot from the Repair option after booting from the XP/2K/NT CD).

However there are a few points to consider:
1. This method can, though not always, correct many/most faulty Win9x file(s).
2. This method may, or may not, cure a virus in Win9x file(s).
3. This method can not cure a boot sector virus or one outside Win9x files.
4. This method will not clear any Win9x clutter, buggy software, or whatever . . .
This method may be quick, but it's not very 'clean'!
It's helpful at times, but is to be avoided if possible.

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Delete the Windows 9x folders/files and reinstall as previously without a format.

This should retain the dual-boot and will suit most users. A boot sector virus is not eliminated.
Clean up C: without destroying the dual-boot (the boot sector and boot files).

All Win9x files & folders must be deleted. Deleting others is optional - recommended.
Program Files is best deleted though you may risk leaving it intact - delete it!
All other files & folders on C: can also be deleted except the XP/2K/NT files.
The C: XP/2K/NT boot files should also be saved to a floppy (make a Rescue Boot Disk).

Remember a new Registry will be created by the Win9x reinstall so all 32-bit software must be reinstalled. Selective retention of software know to be safe should retain saved parts though these are best backed up, the software deleted and reinstalled later.

1. Backup important data, settings, passwords, e-mails, etc.
2. Make sure your Win9x boot disk gives CD access, or copy Cabs to hard disk.
3. Boot to XP/2K/NT and create the Rescue Boot Disk.
4. Delete the Win9x folder, Program Files, all files except XP/2K/NT files on C:.
    Best is: backup XP/2K/NT files from C:\, DELTREE C:\, restore the XP/2K/NT files.
5. Boot the Win9x boot disk to true DOS and reinstall Win9x as it was previously.
    You can use   setup /is
    Do not alter the file system (FAT or FAT32) used by C:.
6. If necessary, copy these boot files from Rescue Boot Disk back to root of C:\
    Boot.ini, Ntldr,, Bootsect.dos, (maybe Ntbootdd.sys, Arcldr.exe, and Arcsetup.exe).

In the unlikely event of failure, read Step 3: below, or read Repair a Dual-Boot.

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Format the C: drive, reinstall Win9x on C:, and fix the boot sector(s).

These instructions assume Windows 9x was installed on C: and XP/2K/NT installed elsewhere.
Read Bootsect.dos and decide if you want to create Bootsect.dos after the Win9x reinstall.

Step 1: Reinstall Win9x
1.1 Boot to XP/2K/NT and create the Rescue Boot Disk (add the Useful Boot Options).
1.2 Make sure your Win9x boot disk gives CD access, or copy Cabs to hard disk.
1.3 Boot the Win9x boot disk to true DOS, and Format C: Do not alter the file system (FAT/32).
1.4 Reinstall Windows 9x on C: as previously. You can use   setup /is   from DOS.
1.5 Copy Boot.ini, Ntldr,, (maybe Ntbootdd.sys, Arcldr.exe, and Arcsetup.exe) from
      Rescue Boot Disk to C:\. Do not copy Bootsect.dos from floppy - not yet, maybe not later.
1.6 Reboot.

Now you have two options:
• Skip to Step 3 if the computer boots straight into Win9x - that's likely.
• Continue with Step 2 if Win9x will not boot - it's unlikely.

Step 2: Recreate Win9x Boot Sector
A valid boot sector for Win9x must be created so it can be saved for the dual-boot.
2.1 Boot with the Win9x boot disk (containing Fdisk.exe and
2.2 At the DOS prompt, type in - and press [Enter] after each line
      FDISK /MBR
      SYS C:
2.3 Reboot. The computer will boot straight into Win9x.
2.4 Step 3 must now be completed.

Step 3: Recreate XP/2K/NT Boot Sector

Assumes Win9x does boot from C: (active), and XP/2K/NT does not boot (installed elsewhere).

The XP/2K/NT boot sector must be repaired and the dual-boot restored.
The XP/2K Recovery Console executes a repair even on an unbootable installation.
If using NT (and not also 2K or XP), read Repair a Dual-boot for instructions on a NT repair.

3.1 Option: Run Btsect.bat from Win9x boot disk to create a new Bootsect.dos.
3.2 Boot from the XP/2K CD or the installation disks.
3.3 At the Welcome screen, press F10.
3.4 Select Repair.
3.5 Select Console.
3.6 Type in & press [Enter]
      FIXBOOT C:
3.7 Type in Exit to exit the Console and reboot. Test.
3.8 Sometimes the MBR must also be fixed from the Console. Type in - and press [Enter]
4.0 Create a new Rescue Boot Disk - but only when the dual-boot is functioning correctly.

If there's still a problem:
Usually there's none. But, if necessary, proceed as follows. Reboot and test after each.
• Boot Rescue Boot Disk & locate which option boots XP/2K/NT. Edit C:\Boot.ini accordingly.
• Copy the XP/2K/NT boot files from Rescue Boot Disk to C:\.
• If C:\Bootsect.dos does not exist, copy Bootsect.dos from Rescue Boot Disk to C:.
• Start over at Step 2. This time run Btsect.bat from Win9x boot disk when at Step 3.1

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Upgrading Win9x in a Dual-Boot with XP/2K/NT should Not be a problem.

Installing the upgrade should not affect the Win9x + XP/2K/NT dual-boot.
Nevertheless, it's sensible to backup those XP/2K/NT boot files first - in case some do go missing.

1. Backup the XP/2K/NT boot files - creating a new Rescue Boot Disk will do that.
2. Bootup to the Win9x to be upgraded.
3. Run the Upgrade.
    Retaining the ability to uninstall the Upgrade is optional. Got plenty of free disk space?

In the event of an unexpected problem, copy the XP/2K/NT boot files back to C:\.
If something extraordinary occurs, execute Repair a Dual-Boot.
The Rescue Boot disk will always boot XP/2K/NT for you in any event.

Be careful if removing an upgraded Win9x dual-booted with XP/2K/NT.

Uninstalling a Win 9x Upgrade in a Dual-Boot:
Save all XP/2K/NT boot files FIRST!
Uninstalling the upgrade may delete Boot.ini. The uninstall may also deletes C:\Bootsect.dos. It is unclear if this applies to all Win9x upgrades. Just play safe.

Uninstalling Win Me in a Dual-Boot:
Never 'Uninstall' Win Me from a dual-boot.
You should edit Win Me out of Boot.ini, and manually delete all Me's folders and files. Win Me's Uninstall.exe restores a backup copy of the Me partition information (stored in C:\Suhdlog.dat). That partition information will overwrite the current sector's!

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Take good care of your boot files and BACK THEM UP WHEN TIMES ARE GOOD!

The boot files for an installed Windows are on the root of the PC system partition. This is nearly always C:, the first partition of the primary drive. This is also where a Win9x/Me boot partition rests most comfortably and it must be FAT/FAT32. The Win9x/Me files can be installed on any other FAT/FAT32 partition, but that OS boot partition must not be converted to NTFS. Many boot files have Hidden, Read-only, and System file attributes. Read Notes, below.

Under a Win9x/Me + XP/2000/NT dual-boot, the Win XP/... is always in control of the boot (nearly always the C: drive). The PC system partition must remain a FAT/32 file system when a Win9x/Me is in the dual-booted (unless using a third-party utility).

It is safer, and advised, to backup the current boot files of an existing Windows before installing the next Windows. And then backup all boot files again after a successfully new installation.

Win XP/2000/NT boot files:
• Boot.ini, Ntldr,, Bootsect.dos, (maybe Ntbootdd.sys, Arcldr.exe, and Arcsetup.exe).
   Bootsect.dos is created by a XP/... install/repair when it recognizes a pre-existing 9x.
WIN9x/Me Boot Files:
• Io.sys, Msdos.sys,, (also Drvspace.bin), and maybe Autoexec.bat & Config.sys.

Ntldr and are not PC-specific and can be copied from any CD or PC.
Boot.ini is PC-specific, but can easily be created, or edited if copied from another computer.
Ntbootdd.sys is specific to a SCSI controller but can be copied from a PC that uses the same.
Bootsect.dos is PC-specific, and cannot be copied. Back it up when it is valid! A Repair may recreate a valid Bootsect.dos. Use to create one if other methods fail.

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Restore BOOTSECT.DOS, or create new one, in a XP/2000/NT + Win9x/Me dual-boot.
Bootsect.dos contains the boot sector for Win9x/Me in a dual-boot with XP/...
This Win9x boot sector file (bootsect.dos) is only used if Win9x is selected from the XP/... Boot Loader menu on bootup. Obviously Win9x can not boot without it. Bootsect.dos is created during the XP/... installation if Win9x is installed first. It may be missing or corrupt. Also, you sometimes need to create Bootsect.dos if XP/... is installed first, and Win9x last.

1. First check if FAT or FAT32 is used for the PC system partition (C:) and OS boot partition (if different). Right-click the drive and select Properties. If it's not the correct FAT/32 file system, then that's the problem and restoring Bootsect.dos will not help.
2. Then try repairing the XP/... boot sector - see this page. This may restore Bootsect.dos

3. Make your own Bootsect.dos:   (read the Bootsect.dos created new page)
Use this only if Win9x is installed on C: (active partition), and Win9x boots normally without a menu (though you can use the SYS C: option in Btsect.bat to make it so, and a XP/2K/NT repair will later fix the C: boot sector XP/2K/NT).
The SYS option creates a NEW Win9x/Me boot sector on C: before Bootsect.dos is created.
• Download (6 KB, freeware) from THPC here (extracts to 17.9 KB).
• Unzip its 3 files to your bootup floppy for installed Win9x. Add to a Startup Disk.
   Other Win9x boot disks must contain Attrib.exe,, Debug.exe,
• Bootup to true MS-DOS with that Startup disk, and run
     Use the SYS option only if appropriate. Then Debug creates a new C:\BOOTSECT.DOS file.
     An existing c:\Bootsect.dos is first saved as c:\Bootsect.PRV. Boot files are also backed up.
Win9x will boot normally. When XP/2K/NT is repaired it will boot, and dual-boot with Win9x.
Note: Bootsect.dos is a Read-only, Hidden, System file (+r +h +s) on the root of C:\.

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Please remember that you alone are responsible for the consequences of any changes you make to your computer hardware or software.

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