I can’t hand in the quest for the rank 3 essence because the NPC isn’t there…
Why is the NPC not there?
From a wowhead.com comment:-
If your quest giver has Zoned out it is because there is a second Flynn in Boralus that is tied to a quest and that NPC needs to be removed.
So, if you have another quest in your log that requires you to hand in to Flynn in a different location, do that, and he should reappear where you expect him for the Worldvein Intelligence Reports.
The only quest in my log is the worldvein one. I have no other quests. 
Edit: Just as I wrote that I figured it out. You need to have completed the starting quests for Tiragarde Sound up to “The Ashvane Trading Company”. He spawns where he’s supposed to after that…
Weird