Merging MySQL Databases

[...] What that statement does is change the INSERT INTO statements to REPLACE INTO statements, REPLACE provides a way to insert data that could be duplicated on a table, deleting a row if it already existed on that table before doing the insert. This will effectively leave on the database the data that was not on the backup and insert in a way that appears only once the data that was on the backup (regardless of the data being or not on the original database). [...]

http://serverprotectors.com/blog/61-64-merging-mysql-databases