So I had not published the project to a cloud repository such as github, and the system on which the files were is gone, however the project is still hosted on fly.io and is live, how do I download the app from fly and get the files back.
It was a laravel project deployment was done using fly io
You can use fly ssh console -a YOUR_APP to start an SSH session and look around the VM for your project (probably in /app). [Edit: actually /var/www/html for Laravel, see below]
Once you find it, you can download it by exiting out of the SSH session and running
fly sftp shell -a YOUR_APP
get /app
Note that there may be differences compared to the original source code (e.g. files ignored using .dockerignore will be missing).