Hey Phil,
As I understand a machine application should be updated this way:
fly m update <machine-id> -a <app-name> -p <internal_port:service_port> --dockerfile ./Dockerfile
You can get the machine Id by:
fly m list -a <app-name>
Here are the links that could help:
Update the Machine’s Docker Image. Fly.io Docs.
Fly Apps on machine prerelease. Fly.io Community.