Okay, trying to cover a few things I've seen in this thread:
The Codex states that characters do not count as part of a unit for the purposes of Resurrection Protocols, meaning you cannot attempt an RP if the only models left are a Lord / Cryptek / joined IC. However, the Ghost Ark states that you nominate "a unit of Warriors". Since the Royal Court member becomes a member of the unit for all intents and purposes (save for RP as that is an explicit exception), then as long as that character is alive, he is still part of "a unit of Warriors".
As for Cryptek / Lord respawning from combat, he can be killed in combat and, due to being Ever-Living, resurrect within 3" of the Ever-Living token (and 1" away from enemy models). No Morale test is taken; Resurrection occurs after Morale, and units that are awaiting Resurrection do not take Morale Checks (or, indeed, interact with the game in any way, shape or form). Thus, there is no way he can come back and immediately be forced to flee; RP is the last thing you do in each phase.
Note you do not generate Ever-Living if the model was destroyed via sweeping advance, Tank Shock or similar; the Ever-Living counter is placed wherever a model is when "removed as a casualty". Sweeping Advance does not state the models are casualties - it simply states the unit is destroyed and removed from the table. Likewise, other "remove from play" abilities would most likely prevent Ressurection Protocols / Ever-Living; they are not 'casualties', but are instead simply no-longer part of the game.