Actually they didn't "lose" it, per the article they have been "stripped" ! USC Trojans stripped of 2004 Grantland Rice Trophy - ESPN Los Angeles
Now if the AP would just do the right thing and disqualify them of the final AP ranking, we'd never have to hear the words "LSU" and "Co-National Champion" in the same sentence.
According to the official NCAA report, the trouble they know of started in the fall of 2004, so there is no impact to the 2003 season nor the bowl win by USC in Jan. 2004, that was the Rose Bowl win over Michigan if memory serves.