Today I performed some complex database merging and the data as well as the table structures had to be compared properly before the production launch.
Following little MySQL query helped me a lot to get the job done.
Here the query will compare ID columns of two tables and return all found in Table_A which it cannot see in Table_B. You can modify the query for different comparisons and enjoy :).
SELECT * FROM Table_1 WHERE Table_1.ID NOT IN ( SELECT Table_2.ID FROM Table_2 WHERE Table_1.ID=Table_2.id )
Hope this will help to your situation as well!