This problem is probably very well known, but since I bumped into it and took a while to find the solution, and even then, the instructions where not very explicit and involved copying files modified by a 3rd party, I decided to write a simple step-by-step tutorial.

I like to dual boot a 9x O.S. with an NT O.S. because of the stability it brings to the table, and it makes it easier to backup/restore Windows 98SE in case things go south, which they frequently do. I chose Windows 2000 to dual boot with Windows 98SE because of several reasons:
- it's more period/hardware correct than XP
- it's not as old as NT4, and it still supports many recent programs
- nostalgia! Awesome memories of playing Starcraft, Quake and Quake 3 Arena on Lan sessions with up to 16 players on Windows 2000 at the University!

At around Service Pack 3 or 4, support for partitions over 127GB was added to Windows 2000. The caveat was, to enable it you had to add the following registry key AFTER installation:

1Windows Registry Editor Version 5.00
2
3[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\atapi\Parameters]
4"EnableBigLba"=dword:00000001

But you can also add 48-bit LBA support to the Windows 2000 Sp4 installation if you follow the following steps:

1. copy the Windows 2000 CD content to a folder in your HDD, ex: C:\WIN2000
2. slipstream SP4 if not yet included
3. run regedit, select a key (ex: HKEY_LOCAL_MACHINE), then File -> Load Hive
4. load C:\WIN2000\i386\SETUPREG.HIV and type a name, for ex: setupreg
5. navigate to HKEY_LOCAL_MACHINE\setupreg\ControlSet001\Services\atapi\Parameters
6. create a DWORD named "EnableBigLba" with value 0x00000001 (1)
7. navigate to HKEY_LOCAL_MACHINE\setupreg, then File -> Unload Hive

NOTE: doing this with Windows 10 x64's regedit doubles the size of the SETUPREG.HIV for some reason, but doing it with Windows XP's regedit leaves SETUREG.HIV with the exact same size as the original, so it's probably better to do it from within XP.

You can now burn the folder back to a CD (don't forget to make it bootable), or install directly from the HDD if you want to dual boot or "upgrade" your current Windows installation. Of course, the motherboard must also support HDDs larger than 127GB, otherwise all this will have been for nothing 😉

On a side note, if you start an unattended installation from CD and you have AutoPartition set to 0 (zero) in the [data] section of unattend.txt, it will ask you where you want to install Windows, but if you start an unattended install from a running O.S. like Windows 98SE, by default it will not ask, it just installs to the same partition, creating a mess of folders and files (like I did). To do an unattended install to a different partition like for example D:, start the installation from the command line or from a batch with the following command:

1WINNT32.EXE /unattend:unattend.txt /tempdrive:D

The /tempdrive parameter redirects the installation to a different drive letter, in this case the D drive. The destination partition must be already formatted in FAT32 if you're starting the installation from an O.S. that doesn't recognize NTFS. I personally use Hiren's BootCD 15.2 (requires more than 256MB RAM) + Disk Management + FAT32 Formatter to prep/format HDDs, and you can automatically convert it to NTFS if you add FileSystem=ConvertNTFS to the [data] section of unattend.txt. If the partition is over 127GB, Windows 98SE must also have support for 48-bit LBA, either by replacing ESDI_506.PDR with a modified one or by installing updated chipset drivers with 48-bit LBA support, otherwise it might mess up the files while writing them to the partition during the 1st step of setup.