This will stop the duplicate numbers. Whether the new numbering will be what you are really after, is another thing:
; WITH cte AS
( SELECT *, 1 AS fldBF
FROM V_qryCSPGA
WHERE fldPK IN(SELECT DISTINCT thePK FROM FN_qryAllDTPK())
UNION ALL
SELECT *, 1 AS fldBF
FROM FN_qryCSGBA()
WHERE fldPK IN(SELECT DISTINCT thePK FROM FN_qryAllDTPK())
)
SELECT *,
ROW_NUMBER() OVER (PARTITION BY fldPK, fldCIA ORDER BY fldPK) AS sCount
INTO #tmpTable
FROM cte
ORDER BY fldPK, fldCIA, fldNDat;