I had a situation playing Hydaspes where the Companion Cavalry were attacked by the elephants. Two swords were rolled; do we ignore the first, hit with the second and throw a rerole for the second only? Or ignore the hit from one but rerole both? I'm guessing the first example.
I remember a discussion about this on the main forum. Short answer is that you ignore the first, apply the second and re-roll only swords that are hits (which would be your first example).
Here's a thread that covers it:
Ignoring sword: a double question