Thus, it is not a bad idea to make your own backup subdirectory on the hard drive and occasionally copy autoexec.bat and its friends to it, particularly when you install new software. Later versions of DOS let you step through autoexec.bat and config.sys line by line. At any point, you can press the Escape key to execute all the remaining lines or press F5 to bypass the remainder. If you're still clueless, you can correct a huge range of dysfunctions just by reinstalliing the missing or malfunctioning software. Computer bundles generally come with a CD that contains all the programs, including the operating system, that are installed on the hard drive, along with utility programs to help you reinstall and recover from a disaster.
Clean installations work for programs, too.
It's better just to replace the damaged files. Sometimes Windows, or programs running under Windows, will give you error messages with the names of files that are missing or unusable. You can't just copy these files from your Windows installation disk, since they are stored in a special compressed format. The program expand.exe, which comes with Windows, lets you copy such files to their proper directory in their correct format. See your manual for more details.