If the data is already in the database then you should be able to do
WITH CTE
AS
(
Select
ROW_NUMBER() OVER(Partition by UniqueColumn ORDER BY UniqueColumn) rn
,<columnlist>
From myTable
)
Insert into BULK Desttable
Select <colunlist>
from CTE
where Rn=1
If its not then you may have to preload it.
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SSC Guide to Posting and Best Practices