Have you had any luck yet find a solution? If not:
1) What program did you use for copying the large files?
2) Can we assume that none of the files were larger than 4gb?
3) What file system is the hard drive formatted in?
4) How many partitions on the hard drive?
5) Any other operating systems installed in the system?
6) Has the system had any trouble keeping track of the time/date?
7) Have you run any malware scans on the system recently?
8) Do you have good backups of your most important data?
I think it might be best to first ensure that your most important data is safe. If you have good backups already, you can skip this step. Otherwise: you can copy data off to removeable disk(s) [if the system is functioning well enough for large transfers], or 'slave' the drive either internally (inside another computer's case) or externally (in an external hard drive enclosure - USB 2.0 enclosures are popular for this) and copy the information that way, or use a disk-imaging program to copy an exact image of your drive, in case data recovery goes badly (gives you more chances to save the data).
During this step, run thorough scans on the drive with up-to-date malware tools. Depending on the health of the drive, this step might not be possible, as large portions of the drive may be unreadable.
Once your data is safely stowed away:
1) Check that the hard drive has some free space available (strange trouble shows up as that space is disappearing)
2) Check in your computer's Bios Setup screens that your Bios settings are OK. Try to get a manual for your motherboard (manufacturer's support sites are good for this, or a quick Google search can help) - if your system's manual isn't clear about the settings, you can refer to Adrian's famous Bios Optimization Guide --- http://www.techarp.com/freebog.aspx
--- check, too, that the time/date are OK and are staying OK. Bios settings that keep changing are a symptom of a weak CMOS battery (the 3v lithium coin batteries only cost about $1.50 USD - if your system has that type). Most systems from the Win98/98se/Me era would be due for a new CMOS battery by now. You'll likely want your drive type set to "Auto", if the Bios is able to recognize the full capacity of your hard drive (if not, and if you aren't using an add-on PCI IDE controller card, refer to the instructions for the "drive-overlay" or "drive-translation" program you are using, for their recommendations [typical drive-overlay utilities: "EZ-BIOS", "Disk Manager"(OnTrack) ... usually installed by "MaxBlast", or "DiskWizard", or such].
3) Run a hard drive diagnostic --- http://www.tacktech.com/display.cfm?ttid=287
--- (might as well test the memory, too, since this is an older system --- http://www.memtest.org
4) If you haven't already, run thorough malware scans. If you scan the hard drive while slaved externally, make sure to run a scan from either floppy or CD - to scan the motherboard's Bios for viruses.
If none of the above seems to be helping, and you need to get the data recovered quickly, while the drive is slaved in another system, point "PC Inspector File Recovery" at the drive & see if it can recover your data = there is a free-for-personal-use version available --- http://www.pcinspector.de/file_recovery/uk/welcome.htm
Best of luck
. . . Gary
[ & Hi There, Geekgirl!]