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When trying to publish data from a folder that has already been registered with the ArcGIS Server, the following error may be returned:
Code=24011 Description="Data source is not registered with the server and data will be copied to the server".
A likely cause for this warning is that the data source of the .mxd being published is referenced with a UNC path, while the data is actually registered with the ArcGIS Server Data Store from a local drive location.
This could also occur in the opposite situation; the data source of the map document that is being published is from a local drive, while the ArcGIS Server Data Store is actually registered with a UNC path.
Confirm the data store's registration for that location. Navigate to the Data Store from the Server Manager or Catalog. For example, in Catalog, right-click the ArcGIS Server connection that is being attempted to publish to, select Server Properties, Data Store tab.
Select the folder where the data is located and click the 'Edit Registered Folder' option (shown with a red arrow on the screen shot below). Confirm that the Publisher folder path matches the data source of the .mxd. After clicking OK, the existent connection path is revalidated.
If the registered location of the data is coming from a UNC path, while in the map document it is coming from a local drive, try the following:
1) Copy the UNC path from the Publisher folder path, and in Catalog create a new folder connection mapped to that location.
2) Remove the layers from the map document and add them back from the new Catalog folder connection.
3) Initiate the publishing process and run the Service Editor’s analyze tool: the warning message that the data is not registered with the server should be gone.