The instructions have been updated to suggest users create their own separate -reduced versions of the font awesome files, instead of replacing the original files on the server. Although this requires just a bit more work in editing templates, it has the advantage of forcing all users to download the new, smaller files, and will not trigger XenForo's file health warnings. Leaving the original files in place will also make it easier to undo your changes if you wish to start using the full font sets again.
Additionally, it is now recommended to edit the preload URLs in the font-awesome-setup template.