Hi partner,
We can create a view to filter all non-merged records, and then create a Duplicate Detection job for this view.
Please refer to https://community.dynamics.com/crm/f/microsoft-dynamics-crm-forum/223601/list-of-merged-records
The Contact entity has a field "masterid" to indicate the ID of the record is was merged into.

This field is not available for conditions in the advanced find, so you won't be able to build a View on this condition.
We will use the "View Designer" tool of XrmToolBox to set the conditions of the view.
First new a Contact view to show non-merged contacts.
This is the download page of XrmToolBox: https://www.xrmtoolbox.com/
After downloading and extracting it, open XrmToolBox.exe.
Use your account to connect to the D365 organization.
Install "View Designer" in the Tool Library.
Open "View Designer", click Open button to select Contact and the new view.

Then click Edit Query button.

Between <filter type="and"> and </filter>, add <condition attribute="masterid" operator="null" />
Then click OK button, click Return FetchXML button.

Finally click Publish button.

Go back to D365, when new a duplicate detection job, select the modified view.
