Arguably, this concern over names could be similar to the AVRO Lancaster. The 1st protype (BT308) started life as the Manchester MK 3 but received its new name shortly after first flight. Perhaps that was a good move considering the notoriety that the Manch had acquired through persistent engine failures.
Correct me if I'm wrong, though; wouldn't making the Nimrod 4 a new Type require a whole new start to the certification process?