It is absolutely legal for a Ghost Ark repair barge to add D3 Warriors back to the unit, for the reason stated above.
The Ghost Ark does not roll a Reanimation Protocol roll, nor does it offer a re-roll (like the Monolith used to do), but has its own rule for creating Warriors and adding them to a unit. It has nothing at all to do with Reanimation Protocols.
The Lords and Cryteks from a Warrior unit are still a Warrior unit even if all the Warriors die, and they still count as Troops. From the example in the OP, if both the Lord and Cryptek die and roll a success on the Reanimation Protocols then they must get back up in coherency and are both still in the same unit. The Ghost Ark can then add Warriors back into this unit.
All that is important is known.