If that doesn't work, command prompt works on exe files, so ipconfig is really a separate program. If you cd to system32 and type dir /w and ipconfig.exe is not there then you need to download it. Also you can set environment variables through command prompt by typing set system root "C:\windows\system32". If none of those work then I don't know what to tell you.
If it has disappeared from c:\windows\system32 you might still have a copy cached in a sub-folder which you can copy back to c:\windows\system32. Note, youy will need to open a command shell as asministrator to do that.
For your environmental variables to have changed, someone or something (another program) would have had to had done it intentionally. There's nothing that I can think of that would have caused your path variable to change by accident or something you unintentionally did unless you issued some commands within the command prompt that dealth with PATH, or were in the Environmental variables in system properties.