I will keep your friend in my prayers.
I'm trying to live a life more in line with my beliefs (I'm a Christian who doesn't always do the best job of living that), and prayer is one of the places where I often find myself at a loss honestly; we can never really "know" if our prayers are being heard, which is where the Faith part comes in, and it is something I struggle with. Particularly when things that seem so incredibly unfair, like the illness of good people that are friends, come into the life equation.
I know you're an Agnostic, and I respect that and am in no way, shape, or form trying to preach to or evangelize to you. Just know that struggles and confusion on the nature of God and prayer and its efficacy are something that even those who are Christian deal with at times.
I sincerely hope your friend is on the mend, and I will keep them in my prayers. Hope this helps, both you and your friend.