Hardrivehelp

ok, this is kinda long and im a noob but whatever. i bought a dell computer about 2 years ago and just a few months ago, i got a virus the and the file in C:/ windows/system32/config/system was deleted. when i bought the computer i also bought like a $400 warrenty so dell sent me a new hard drive. they never asked me for the old one back. i tried calling but they had no record of it. so now i have a new hard drive and an old one with a missing file. so i have this win98 emachines that has been sitting in my basement for some time and have set it up. the emachine computer has a crappy 4gb hard drive and i tried to put in my old dell hard drive for more memory. i still get the same error message that the file is missing or corrupt. is there any way to copy the file from the new to the old hard drive since they are the same? or somehow use the 4gb hard as the OS and the old dell one just for storage? thanks for any suggestions