A. First, the cause could be a fatal system crash. To determine whether a fatal crash occurred, transfer the hard disk to another system and test to determine whether the disk works properly.
A second possibility is a ROM-based virus. Such a virus could hide hardware from the OS. To evaluate whether such a virus is the problem, you need to run a virus scan program from a 3.5" disk. If a virus is indeed to blame for the crash, you need to run a repair process from a bootable 3.5" disk.
Lastly, the hard disk might have bad sectors that you need to fix. You can boot to a DOS 6.2 3.5" disk, then use Microsoft Diagnostics (MSD) and the Fdisk command to determine whether the system is detecting the hardware properly. (MSD reports about hardware, and Fdisk reports about partitions.) If bad sectors are indeed the problem, I suggest you reinstall NT and restore a recent backup.