What you can do is after import copy the data to another table that has an identifier field.
With the next statement you can determine the doubles and know by the unique ID that you can delete the doubles
after that you can set them into the table that needs the data
select uniqueID, EmployeeID FROM
(
select Row_Number() over(partition by EmployeeID order by EmployeeID) as Rowno, uniqueID, EmployeeID from MyTableWithUniqueIDAdded
) as t
where t.Rowno > 1
clear enough?