Hi, I've done a little simulation on my part and here is I think, a legal way (as far as Microsoft is concerned) to fix it.
1) Boot up your PC in MSDOS mode with CDROM support.
2) Load the installation CD for WIN98.
3) Change your current driveand directory to the folder where the cabinet (.CAB) files of the installation is located (usually the root directory of the CD)
4) Type in the following:
extract win98_25 /l c:\ win.cnf (press enter)
5) This should extract the WIN.CNF file to the root directory of your C: drive.
6) Go back to your C: drive and type in the following:
copy win.cnf c:\windows\win.com
7) The WIN.CNF will be copied to your windows directory as .COM file.
Well, I hope that helps!