It appears that changing the data transfer rate (throttle) settings for SnapMirror in System Manager does not impact a running SnapMirror, and that the only way to modify a running SnapMirror session is via the CLI. I would like to suggest that the GUI either indicate that this is the case or provide an option to modify the running SnapMirror. The current situation of indicating that the throttle setting has been changed when it actually hasn't constitutes an issue with the product, especially since there's no way in Data OnTAP to see what the actual running SnapMirror throttle rate is for a given session.
System Manager does not support changing the throttle time for a running snapmirror relationship, it will be applicable for the next one.
But your point is fair, we should indicate that if the snapmirror relationship has an active transfer going on and user changes the throttle, GUI should tell that this will not be applicable for current transfer but for the next one.