|"When you re-installed, did you perhaps select the Fat32 file system? That could explain why the "new" XP can't "see" the backup files on a backup HDD that is NTFS.|
It doesn't matter whether Windows is installed on a FAT32 partition and other drive partitions are NTFS - XP can see the NTFS partitions fine.
When hard drives were smaller , I used to make a FAT32 partition on the drive for Windows that was a tiny bit under 32gb (so that the allocation unit size - minimum data space used by a file - was 16kb rather than 32kb), and make other partitions either FAT32 or NTFS and I had no problems accessing any NTFS partition.
"windows is now on F drive for some reason"
2000 and XP assign the drive letter to the partition Windows itself is installed on in alphabetical order starting at C according to whether Setup detects other partitions that have been already assigned drive letters when Setup is run. E.g. If Setup doesn't detect other such partitions, it uses C for the partition Windows is installed on. If the drive you didn't unplug had already had C, D, and E assigned to other partitions, and you didn't delete the partition that was assigned C and install Windows on that one, Setup uses F for the partition Windows is installed on.
If the other partitions are on the same hard drive, you can get around that by using something such as Partition Magic to hide all the partitions you don't want Setup to detect, then unhiding them after Setup has completed.
Vista's, and probably Windows 7's, Setup , on the other hand, always uses C for the first installation of Windows for the partition Windows is installed on no matter what other existing partitions it detects during Setup. Vista's Setup detects partitions hidden by Partition Magic.
Is the other hard drive you unplugged an external drive?
If it is, that's a different subject, and your data may still be there.
When you unplugged the other hard drive, assuming it was internally connected, did you have the power cord disconnected to the computer, or the AC to the computer otherwise switched off ?
OR - did you have the the power cord disconnected to the computer, or the AC to the computer otherwise switched off , when you plugged the drive in agian ?
IF you didn't, that may be why you data seems to be gone. ATX power supplies are always powering some wires as long as the power supply is receiving live AC.
Test that hard drive with drive manufacturer's diagnostics.
See the latter part of response 1 in this:
(thanks to Dan Penny for this link:)
Hard Drive Diagnostics Tools and Utilities
If you don't have a floppy drive, you can get a CD image diagnostic utility from most hard drive manufacturer's web sites, but obviously you would need to make a burned CD, preferably a CD-R for best compatibility, on another computer if you need to.
If the hard drive itself tests okay, any data problems found can be fixed, one way or another.