Referring back to these posts re DT3 which confirmed that when using Custom Metadata, outgoing links are not showing in the links inspector, whilst incoming links do. The new graph shows both of these correctly as Item Links.
So the links are there, but the links inspector is not picking up one of them.
Outgoing links in the Document > Links inspector are limited to the links found in the body/text of the document. Selecting one shows it in the document, deleting one removes it from the document.