I have a 40 GB disk with this partitioning scheme:
Three primary partitions and one extended

1. 4GB Windows 2000 (NTFS)
2. 3GB Win 98 SE (FAT32)
3. 1G DOS 6.22 + Win 311 (FAT16)

Extended partition contains
4. 6GB Win XP (NTFS)
5. 20GB FAT32 for data
6. rest linux (EXT2)

I have read and verified that DOS's boot sector cannot boot IO.SYS etc if the
dos partition starts above the first 2GB of the disk. However, if I boot from
floppy my dos partition is visible because it is still below the 1024 cylinder limit (below 8 GB).
I use Win 2000 boot loader (boot.ini). I have put the boot sectors
of the OSs in a seperate file but dos cannot boot with this configuration.
I don't want to put dos first bacause it will always be in drive C:
Where can I find an updated boot sector which can boot dos if it's partition
is above 2GB? Or how can I patch the boot sector to do it?

http://www.paragon-gmbh.com/f_bm.htm

http://www.ranish.com/part/xosl.htm

40GB HD is NOT a problem at all for DOS! DOS (newer versions) should at least recognize 2048GB FAT32 drives. Only *older* versions of DOS (like 6.22) won't support drives above 2GB! Please read the following thread for more information:

http://www.computing.net/dos/wwwboard/forum/14128.html

For example, split your 40GB HD into two 20GB FAT32 partitions:

C: FAT32, 20GB
D: FAT32, 20GB

Then install MS-DOS 7.10 or similar (e.g. FreeDOS Kernel 2032). Then DOS will see and access all data on your HD!