I'd suggest to implement a new feature:
create a new attribute: "Hook to GUI element"
for each freemind map opened
display notes as pop-up window if they have the "Hook to GUI element" attribute that matches the front most window of another program.
This would be some-way equivalent to the old "New notes" software that displayed notes related to a window name, program reference, or would appear if some character string partially match the window title.