Use the IBM® Integration API to remove connections between nodes.
The following example shows how you can disconnect two nodes:
File msgFlow = new File("main.msgflow");
MessageFlow mf1 = FlowRendererMSGFLOW.read(msgFlow);
MQInputNode mqinNode = (MQInputNode)mf1.getNodeByName("My Input Node");
MQOutputNode mqoutNode = (MQOutputNode)mf1.getNodeByName("My Output Node");
mf1.disconnect(mqinNode.OUTPUT_TERMINAL_OUT, mqoutNode.INPUT_TERMINAL_IN);
MessageFlow mf1 = patternInstanceManager.getMessageFlow("MyFlowProject", "main.msgflow");
MQInputNode mqinNode = (MQInputNode)mf1.getNodeByName("My Input Node");
MQOutputNode mqoutNode = (MQOutputNode)mf1.getNodeByName("My Output Node");
mf1.disconnect(mqinNode.OUTPUT_TERMINAL_OUT, mqoutNode.INPUT_TERMINAL_IN);