SSH Keys were changed/regenerated on Hetzner cloud server, I got alert "remote host identification changed"

As comments suggests, the answer is cloud-init package. It's responsible for re-initialization of images of virtual machines, and one of the steps for initialization is re-generation of host's ssh keys.

It's done once 'per instance' based on reported change in instance ID (what is 'instance ID' is highly dependent on cloud provider, or even on ID on "NoCloud" provider for baremetal).