An update was released for Final Fantasy 9 today on Steam, and users reported it removed game files from their PC.
According to various Steam users who own Final Fantasy 9, the latest patch essentially removed everything but the launcher.
If you look on SteamDB, you can see the list of files removed with the patch.
But don't fret just yet, as it seems Square is updating the game once more, and the most recent was made just 40 minutes ago.
It's suggested you don't fire up the game until the issue is resolved.
Just consider this a heads up.