We're investigating an issue where fly deploy is creating new Fly machine instances rather than updating existing ones, leading to apps with a mixed state. We're currently investigating the issue.

As a workaround, please try removing the "processes = [ "app" ]" line from your fly.toml configuration file and redeploying. Another workaround is to downgrade flyctl to 0.4.40 - this should resolve the issue in the meantime.