Use this code:
WebClient myClient = new WebClient();
myClient.DownloadFile(yourLink, YourFileLocation);
This should overwrite the file with the new one.
----EDIT #1
WebClient myClient = new WebClient();
myClient.DownloadFile("https://website.com/test.exe", @"C:\test.exe");
This should replace the test.exe on your computer with the test.exe from the website.
----EDIT #2
To replace the file on someone else's computer, you would make sure that when the file is downloaded, it is always in the same place on every computer. Here is an example of putting it in "My Documents"
WebClient myClient = new WebClient();
myClient.DownloadFile("https://website.com/test.exe", @"C:\Users\" + Environment.UserName + @"\Documents\test.exe");