The flags have finally come back. After an hour of finding them, installing them, and manually adding them to each user that has been active within the past few days, they should show up.
If they don't (or if you haven't logged in recently), edit it yourself.
Only countries current members are from are on the list. If you are new and your country is not available, let an admin know. These include the United States, United Kingdom, Canada, Australia, Germany, Ireland, Peru, Greece, and Scotland.