--DELETE FROM inohis
SELECT * FROM inohis
 WHERE (iobit = '2' AND trn_date = '20161130')
    OR (iobit, trn_date, trn_seq, ino_seq)
    IN (SELECT b.iobit, b.trn_date, b.trn_seq, b.ino_seq
          FROM inohis a
         INNER JOIN inohis b
            ON b.iobit    = '1'
           AND b.trn_date LIKE CONCAT(a.in_date, '%')
           AND b.trn_seq  = a.trn_seq
           AND b.ino_seq  = a.ino_seq
         WHERE a.iobit    = '2'
           AND a.trn_date = '20161130'
        )
;

IN 절에서 다중컬럼을 지원하지 않는 모양이네요.
Exists 구문으로 바꿔봤습니다.
 

--DELETE FROM inohis b
SELECT * FROM inohis b
 WHERE (iobit = '2' AND trn_date = '20161130')
    OR (iobit = '1' AND EXISTS
       (SELECT 1
          FROM inohis a
         WHERE a.iobit    = '2'
           AND a.trn_date = '20161130'
           AND a.trn_seq  = b.trn_seq
           AND a.ino_seq  = b.ino_seq
           AND a.in_date  = LEFT(b.trn_date, 6)
        )
        )
;