Strangely there is no (at least documented) UnregisterWindowMessage function to ensure that no more notifications of that message will be sent and handled between both applications.
Can a message that was registered using RegisterWindowMessage be unregistered or not?
There's no UnregisterWindowMessage and no alternatives like GlobaladdAtom/GlobalDeleteAtom available. To ensure that no more notifications are handled you could register and use a 'HANDLE NOTIFICATIONS OFF/ON' type of message.