Du kan göra detta med en lagrad procedur
DELIMITER $$
CREATE FUNCTION strSplit(x VARCHAR(65000), delim VARCHAR(12), pos INTEGER)
RETURNS VARCHAR(65000)
BEGIN
DECLARE output VARCHAR(65000);
SET output = REPLACE(SUBSTRING(SUBSTRING_INDEX(x, delim, pos)
, LENGTH(SUBSTRING_INDEX(x, delim, pos - 1)) + 1)
, delim
, '');
IF output = '' THEN SET output = null; END IF;
RETURN output;
END $$
CREATE PROCEDURE BadTableToGoodTable()
BEGIN
DECLARE i INTEGER;
SET i = 1;
REPEAT
INSERT INTO GoodTable (col1, col2)
SELECT col1, strSplit(col2, ',', i) FROM BadTable
WHERE strSplit(col2, ',', i) IS NOT NULL;
SET i = i + 1;
UNTIL ROW_COUNT() = 0
END REPEAT;
END $$
DELIMITER ;