MNE cannot be configured to automatically delete emails from the Notes source mail file after they are successfully migrated.
This is by design. MNE is a non-destructive migration tool and does not remove source mail items after copying them to the target.
There is no supported MNE setting to delete successfully migrated source emails.
If source cleanup is required, complete and validate the migration first, then remove the source items outside of MNE using an approved Notes/Domino administration or retention process.