If you replace the file, make sure you use the Replace Media tool (Media > Library > Hover over the file and choose Replace Media). If you were to just upload the new version without doing the replacement, you will start to compile duplicates, and you may run into some confusion later on. 

If you want to replace a file with an updated version, follow these steps:
  1. Hover over the file in the Media Library that you want to replace
  2. Choose Replace media
  3. Click “Choose file”
  4. Choose the new file
  5. If the image is attached to any type of Page or Post, you will want to “Replace the file, use new file name and update all links”.
  6. Click “Upload”