If you press R to start the Repair process after booting the Windows 2000 CD-ROM or four boot floppies, you are greeted with a message similar to:
Windows 2000 Professional Setup Setup has found Microsoft Windows 3.0 or 3.1 or Windows for Workgroups 3.11 in the following folder: C:\Windows Setup can install Windows 2000 into this folder. If you install, you will have to specify new settings and reinstall your applications. To install Windows 2000 into this directory, press ENTER. Caution: do not select this option if you need to use an older version of Microsoft Windows. To select a different folder for Windows 2000, press N.If you have Microsoft Windows 3.x installed and it's folder is in the path in the Autoexec.bat file, the above happens. If you press Enter, Windows 2000 will be installed in this folder, overwriting Windows 3.x. If you press N, you can start the Repair or Recovery Console.
The only way to prevent the message is to remove the folder from the path in Autoexec.bat, but to start Windows 3.x, you will have to manually change to the folder.