hey there friend.
from the picture, the red beam ends look only minimally rotted/punky.
i would consider redesigning this so that the ends of those "brackets are INSIDE the barge rafter, with the barge rafter nailed through the face into it.
otherwise there's no way to keep it from rotting over time.
check this out:
read the "alternative bracket connection..."
or at least figure out a way to bevel the ends and caulk it up real well.
from the picture at least it looks like minimal damage. i wouldn't go ripping the whole thing out. it must go into the house at least a few feet.
cool house, BTW.