That's an easy technical question, but maybe a more difficult policy question. Technically, you can do this in one of two ways:
1. Edit the galley. Log in as an Editor; from your Archives queue, find the submission and go to its Editing page. From there next to each galley you've uploaded you'll see an Edit link. Click that, and you'll be able to upload a new file to replace the old file. One caveat about doing it this way: unless you add text to the effect that this article has been updated since publication, your visitors won't know that it's been updated.
2. Replace the galley. Do the above, but instead of clicking the galley's Edit link, Delete the galley. You can then upload new galleys to replace those you have deleted. This will generate new final URLs to the galley, which may not be desirable especially if the galleys have already been linked to. This won't explicitly demonstrate that updates have been made, either, although expert users will notice that the galley ID has been incremented by 1, suggesting that it is not the first such galley.
Policy-wise, my suggestion would be to go with process 1, but add text at the top of the galley indicating that the file has been updated, and how. That way the author is happy, but folks know that the file has been modified.
Questions or comments welcome!