I found some more info on this. Yahoo! will be changing maddux's (and Hanley Ramirez's) numbers on Sunday to reflect the scoring change.
If you go to your Yahoo league page and add 'statcorrections' to the end of the url you will see the items come up.
However, there is a line at the bottom of this page that says if a correction is made after a current week, they will not change head to head results, so this will only effect roto leagues. Still, this lowers my team ERA by 4 points, from 3.90 to 3.86. Considering the guys next to me are 3.82 and 3.96, this is huge.