Can I ask why it's necessary to kill ALL spectral dragons? Shouldn't you only kill those guarding the Chains of War?
As far as I remember, there are two ways to complete this mission: either eliminate
all the twilight dragons and then go after Nicholas. In that case, he won't be resurrected. Or...
Phoenixes are only needed for the quest, so it's best to keep them in reserve, as you need 5 phoenixes to kill Nicholas, and they must not be resurrected.
...attack Nicholas with phoenixes, but to prevent him from resurrecting, it's enough to have one live phoenix left at the end.