How do I delete only related records in a multi-key MERGE in SQL Server?
You can filter out the rows you need to consider from the target table in a CTE and use the CTE as the target in the merge.

WITH T AS
(
  SELECT M.LeftId, 
         M.RightId, 
         M.CustomValue
  FROM @Mappings AS M
  WHERE EXISTS (SELECT *
                FROM @Values AS V
                WHERE M.LeftId = V.LeftId) 
)
MERGE T
USING @Values AS S
ON T.LeftId = S.LeftId and
   T.RightId = S.RightId
WHEN NOT MATCHED BY TARGET THEN
  INSERT (LeftId, RightId, CustomValue) 
  VALUES (S.LeftId, S.RightId, S.CustomValue)
WHEN MATCHED THEN
  UPDATE SET CustomValue = S.CustomValue
WHEN NOT MATCHED BY SOURCE THEN
  DELETE
;