Hi Joe,
You are right that changing a connection that is already registered in a copied system can influence of the original connection, as both consumers have the same registration handler to the producer portal.
The instructions on how to perform copy when having FPN configured is documented in the following document:
How to Copy SAP Systems in a Federated Portal Network
The reason for disabling the ability to edit registered connection, was that many customers used it to change connections, after they were registered, with no relation to system copy, and that caused many issues.
Hence it is not going to be reverted.
Thanks & regards,
Michal