Use the IBM® Integration API when developing message flow applications to rename message flows.
File msgFlow = new File("main.msgflow");
MessageFlow mf1 = FlowRendererMSGFLOW.read(msgFlow);
mf1.setName(mf1.getName()+"Generated");
MessageFlow mf1 = patternInstanceManager.getMessageFlow("MyFlowProject", "main.msgflow");
mf1.setName(mf1.getName()+"Generated");