Not sure exactly why the logging spam wouldn’t go away after you deploy your app with this issue fixed…
Not that I recommend it, but you can always flyctl ssh console -s ... into your app instances (ref), and sudo things to your heart’s content.
You can also scp things (see), fwiw.
See if those come in handy?
Just a note, you could use Fly’s built-in vault to vend secrets, btw.