To reproduce (with no active subscriber):

1. apply a hot fix on a yaml configuration, e.g. change template title
2. check that changes were picked up
3. delete a hotfix (the node is not marked as deleted because there is no active subscriber)
4. changes are still there

After some further investigation, the issue apparently affects only configuration files, not templates, as one can see in the attached screencast where we tried to reproduce the issue. In particular, after removing a hot fix, the original configuration is not reloaded at YamlConfigurationSource#loadAndRegister. That should be triggered at LayeredResourceOrigin.RelayingChangeHandler#onResourceChange starting at line#294 but the condition to trigger the onResourceChanged method is never met.