I've never had an issue of this sort before but after, I'm glad I had my old Gateway system's hard drive duplicated on a few other drives. I used my Dell with Windows 7 to copy a zip file with some drivers to a floppy disk and when I put the floppy into the Gateway and tried using DOS to copy the zip file to it's hard drive, it suddenly became the only file on the entire hard drive was that zip file. Did the same thing when I swapped that hard drive. However, after getting everything restored from another backup drive (I'm pretty paranoid with older hardware so I keep a few drives I can easily swap in and continue like nothing happened), I used Win 3.11's file manager to copy and no issues.

I'm not sure of the cause of this glitch but I was able to make it repeat multiple times.