When you make a change to the existing NSG rule to block the traffic, the flows which are active will still be running and will not be terminated. Any new flow will hit that rule and that gets blocked. It has nothing to do with the effective Security rules. Also, when you make changes, give it a 30 seconds for the system to populate the change all the way in the stack to get it working.
Let me know if you have any questions.
Regards,
Karthik Srinivas