I have questions!
Is this logical drive a boot drive for one of the OS's?
If it's not a boot drive, do you have applications installed on it that are seen between the two OS's - in other words, is the drive letter critical to both sides of the dual boot?
What is the status of the drive in Disk Management? Is it showing as "foreign media" or as unformatted, or simply not there?
Courses of action I'd consider:
Before you go any further, please verify that the backups on the external drive are really there, and that the dates are current, and that the backup software can open and look inside the actual backups (act like you're going to restore, just don't click the final OK). If anything looks hinky, back up the drive again from the partition that can see the missing data.
If the drive is showing as "foreign media" or "unknown", right click it and see if the option to "import foreign media" is available. If it is, do so and see if that rebuilds the drive data in that partition.
The health of this drive is very questionable at this point, I would not bother restoring data to the partition. I'd seriously consider replacing the entire drive. Acronis True Image or Norton Ghost can be used to image the partitions to another drive. It's likely Ghost could do all the partitions, recovering the "missing" data as it goes.
I'll dig around a bit for antivirus software, my "default" free AV is AVG. I'm a little WTF about the AVG on the Win2k.
You can PM me or email if you want. I'm happy to help.