Hi,
Is the MongoDB hosted elsewhere or are you running that as a separate app in Fly?
EDIT: Whoops, didn’t see MongoDB Atlas in the title.
If it’s just cron and bash stuff to work with your Mongo data, you could use GitHub - fly-apps/supercronic: Run periodic jobs on Fly with supercronic instead.
Health checks:
Removing them from your fly.toml will not stop them, and that they’ll happen anyway.
Ref: Failing Health Checks after Deploy - #4 by kurt
Maybe you can ‘fool it’ with a custom health check script, as shown here?