Replacing files is easy once you know the trick...

  1. Click on the file number
  2. Follow the link to "upload a new version of this file"
  3. Upload the new file - you can name the new one any way you like (keep it the same or change to something new - it makes no difference)
  4. When you see the little [B] next to the file description, you will know your replacement was successful

It might appear to be the old version if you view without being logged in for a couple of days due to the site's cache being updated, but the new one is what will actually download.
That's all there is to it.