Prayer or devotion does not affect the karma of the body. No, it doesn't. I feel it can affect in many different ways. When you do good things, many things happen. One is the grace of God with you. Second, our past karma is a whole storehouse. If you notice, Sridhama Krishna's body passed away due to throat cancer. Ramana Maharshi had tumor. And that's the way they died,. But throughout their lives also, little problems ups and downs kept coming. So this whole going beyond the causality of karma is only to realize that you are the ultimate.