Is he using the solderless adapter? The same thing happened to me, and I just opened up my Xbox and re-tightened the screw down that holds the solderless adapter to the motherboard.
Sometimes it "springs up" a bit and loses contact with the LPC points.
However, my Xbox was flashing red and green, not just green so it could be something else as well.
I'd definitely check and make sure the solderless adapter is making solid contact with the LPC points and that the D0 wire is still in the hole before messing around with the EEProm.