I think this is mostly expected behavior with Databricks Asset Bundles, not really a bug.

In bundle deployment, the local bundle config is usually the source of truth. So when you change databricks.yml or any included YAML locally and run deploy, Databricks uses that YAML to update the actual resources like jobs, pipelines, variables, permissions, etc. But the YAML file itself may not always show up in the remote workspace the same way .py or .sql files do.

Few things I would check:

1. Is that YAML file included in the main databricks.yml using the include section?
2. Run databricks bundle validate -t <target> and see if your local change is actually getting picked up.
3. Deploy from the bundle root using databricks bundle deploy -t <target>.
4. Avoid changing the remote YAML directly during development, because then it becomes confusing which version is the real source  local or remote.

My usual approach would be: keep YAML changes local/Git-based, validate, deploy, and then verify the actual deployed job settings rather than only checking whether the remote YAML file changed visually.

So in your case, I would first confirm whether the YAML is part of bundle config or just a synced file expectation