Thanks for using Logflare 
Okay we have a pull request in to add Logflare to the fly-log-shipper but you can use our fork until that happens!
I would suggest keeping the Logflare logger going as is, and not using the console Logger backend in your prod Elixir config. The log shipper should pickup everything until Logger gets started, and then after that the Logflare Logger backend will take over.
I would also suggest using two different Logflare sources. One for the Fly logs, and one for the Elixir logs. They will have different payload shapes and it will be easier so as to not clash schemas.
I’ll work on cleaning up the Fly logs a bit with an example fork at some point. Just need to remap things a bit more.