Попробуйте это:
SET NOCOUNT ON
DROP TABLE #Relations
CREATE TABLE #Relations(ID int, way_id int, node_id int, sort int)
INSERT INTO #Relations VALUES (16997, 107187465, 1232361697, 1)
INSERT INTO #Relations VALUES (16998, 107187465, 1232361496, 2)
INSERT INTO #Relations VALUES (16999, 107187465, 1232361625, 3)
INSERT INTO #Relations VALUES (17000, 107187465, 1232361954, 4)
INSERT INTO #Relations VALUES (17001, 107187465, 1232361625, 5)
INSERT INTO #Relations VALUES (17002, 107187465, 1232361937, 6)
INSERT INTO #Relations VALUES (17003, 107187465, 1232361302, 7)
INSERT INTO #Relations VALUES (17004, 107187465, 1232361878, 8)
INSERT INTO #Relations VALUES (17005, 107187465, 1232361365, 9)
SET NOCOUNT OFF
SELECT id, way_id, node_id, sort
FROM #Relations
WHERE (way_id = 107187465)
DELETE
FROM #Relations
FROM #Relations
JOIN (
-- select minimum id: this we'll keep
SELECT MIN(#Relations.ID) Id,
#Relations.way_id,
#Relations.node_id
FROM #Relations
JOIN (
-- get all duplicated rows
SELECT way_id, node_id
FROM #Relations
GROUP BY way_id, node_id
HAVING COUNT(*) > 1
) duplicates
ON #Relations.way_id = duplicates.way_id AND
#Relations.node_id = duplicates.node_id
GROUP BY #Relations.way_id, #Relations.node_id
) stay
ON #Relations.way_id = stay.way_id AND
#Relations.node_id = stay.node_id AND
#Relations.id != stay.id
-- comment next line to remove all duplicates
WHERE (#Relations.way_id = 107187465)
SELECT id, way_id, node_id, sort
FROM #Relations
WHERE (way_id = 107187465)