There can be problems. Windows 2000 setup does not verify that BIOS INT-13 extensions are enabled or available for use. If they are not, upon reboot, you will get the following error message after POST:
A disk read error occurred.
Press Crtl+Alt+Del to restart.
A similar problem occurs with SCSI controllers when drive translation is disabled and INT-13 extensions are disabled in the SCSI BIOS.
In either case, with these features disabled, the drive's geometry is native and the drive's partition table will contain Cylinder, Head, and Sector (CHS) values which cannot be described within the partition table's upper limit of 1,023 cylinders. INT-13 extensions must be used to boot from the partition.
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Setup Cannot Continue After Reformatting Dynamic System/Boot Partition
Details how to use Dskprobe.exe to edit the Partition Table volume data to fix untranslated offsets (int13 translation problem)