Check this page out: https://web.archive.org/web/20150329004325/https://dev.mysql.com/doc/refman/5.0/en/insert-on-duplicate.html
At the bottom of the page they explain how you can make LAST_INSERT_ID meaningful for updates by passing an expression to that MySQL function.
From the MySQL documentation example:
If a table contains an AUTO_INCREMENT column and INSERT … UPDATE inserts a row, the LAST_INSERT_ID() function returns the AUTO_INCREMENT value. If the statement updates a row instead, LAST_INSERT_ID() is not meaningful. However, you can work around this by using LAST_INSERT_ID(expr). Suppose that id is the AUTO_INCREMENT column. To make LAST_INSERT_ID() meaningful for updates, insert rows as follows:
INSERT INTO table (a,b,c) VALUES (1,2,3)
ON DUPLICATE KEY UPDATE id=LAST_INSERT_ID(id), c=3;