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When republishing an existing metadata document to a metadata service, an additional copy of the document is added to the service when the user does not have write access to the source metadata document (XML file).
Every metadata document published to a metadata service is assigned a unique ID that is written to the source metadata document when it is first published. If the user does not have write access to the source metadata document, the ID can not be written to it. As a result, when the user republishes the same metadata document, the metadata service can not compare the ID with the IDs of documents already published; the metadata service assumes the document is a new metadata document.
Ensure the user has write access to the source metadata document so the metadata service can assign it a unique ID. When the service republishes the document, it will replace the existing document.