SELECT
	*,
	DENSE_RANK() OVER(PARTITION BY ORDER ORDER BY [Date]) AS Reference
FROM
	YourTable

;with cte as
(
	SELECT
		*,
		DENSE_RANK() OVER(PARTITION BY ORDER ORDER BY [Date]) AS NewReference
	FROM
		YourTable
)
UPDATE cte SET Reference = NewReference;

UPDATE t
SET Reference = COALESCE(t1.Cnt,0) + 1
FROM YourTable t
OUTER APPLY (SELECT COUNT(DISTINCT Date) AS Cnt
             FROM YourTable
             WHERE Order= t.Order
             AND Date < t.Date
             )t1