Not sure, but I feel this is what you are after

SELECTL01, LO3, COUNT (*) Counts

FROM(

SELECTA.L01, A.L03, A.L39, B.A04, B.A10, B.A31

FROM[LEARNER_SN05]AS A

INNER JOIN(

SELECTL01, L03, A04, A10, A31

FROM[AIMS_SN05]

WHEREA04 <> 35

ANDA10 IN (10, 22, 81)

ANDA31 IS NOT NULL

GROUP BY L01, L03, A04, A10, A31

) AS B ON B.L01 = A.L01 AND B.L03 = A.L03

WHEREA.L39 = 95

GROUP BY A.L01, A.L03, A.L39, B.A04, B.A10, B.A31

)

GROUP BY L01, L03

HAVING COUNT( * ) > 1