Methods for inhibiting disruption of the healing process in a hollow body organ such as a stomach that is physically modified to restrict or reduce its food receiving capability are described. A physical boundary is used to form the stomach modification. An inlet portion of the modified stomach communicates with the esophagus and an outlet portion of the modified stomach communicates with the small intestine. A bypass shunt is inserted into the modified stomach alongside the physical boundary. The shunt enables food to pass from the esophagus through the shunt to the small intestine thereby reducing food and fluid contact with the physical boundary, and reducing pressure and tension forces at the physical boundary that establishes the stomach pouch. The shunt is inserted during the stomach modification procedure.