Yes, long running VMs without a web service are supported. Just remove the [services] block from your fly.toml.
There’s no strict uptime guaranty, but these should be pretty stable. It is more likely a VM on Fly shuts down than one at, say, DigitalOcean. But we don’t systemically turn VMs off.
VMs will shut down when:
Hardware fails
If there are extreme capacity issues in a region, larger VMs get priority (this has happened once, ever).
Your processes can definitely run for weeks. You can also set kill_timeout to give some control over shut down if we ever deliberately turn a VM off.