If you want to change your message flow while you are debugging it, you must redeploy it to the integration server, then reattach the flow debugger.
Stop the message flow before you redeploy it. See: Debug: stopping a message flow instance
During your debugging session, you might find a problem in a message flow that you want to correct or see a behavior that you want to change. You can alter the flow to resolve the situation and redeploy the flow to the integration node: