The damage that you are seeing is caused by a bacterium named Pseudomonas syringae. This pathogen causes a disease on cherries and other stone fruits called bacterial canker. As the name implies the disease causes a canker, or a dead area, in the branch or trunk that interrupts the flow of water and nutrients to a branch or, if the canker is on the trunk, to the entire tree. Unfortunately, very little can be done to save the tree if the canker is in the trunk. If there is only a new canker in a branch it may be possible to remove the branch. Be sure to remove the entire branch at its base because the bacterium may have already moved below the visible canker. Some people believe that there is a benefit of cutting longitudinally through the canker, thereby relieving the pressure on the canker and allowing the tree to wall off the infection, but there is no scientific data to support this remedy. Looking at the severity of the infection it might be best to remove the tree and plant a new one in its place if you want to continue to harvest cherries. It is especially important to remove all potential inoculum if you have other stone fruit or even pear trees in the area that might become infected. The best remedy to prevent future infection is to never prune within 7 days of a rain event and keep the tree moderately vigorous. For more information about the disease click on this link. http://pnwhandbooks.org/plantdisease/cherry-prunus-spp-bacterial-canker