My Ontology Object Type is set to apply the most recent value for the conflict resolution.
When a particular record no longer exists on the backing dataset, the delete doesn’t flow through the ontology and it still exists there.
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Reference these docs to check expected behavior based on your specific situation.
Based on the docs, your problem might be that the record that was removed from the dataset was at some point either created in the ontology directly (this is possible if the object was created before it appeared in the backing dataset and had the same id) or was deleted and recreated in the ontology directly. If this was the case, the object would still be present in the object set despite disappearing from the backing dataset, even when using the “apply most recent value” conflict resolution strategy.
It is also possible that the most recent sync of the backing dataset to the ontology failed — you can check the status in the “datasources” tab of the object type configuration in ontology manager.
Hope this helps!