I finally managed to get the key from Tol Dagor needed to complete this quest for the Pride of Kul Tiras. However, upon returning to the Harbormaster’s Office, Flynn isn’t there. I found him near the expedition table at Bridgeport, but I cannot turn in my quest to him; I think because he’s not technically in the office needed to fulfill the requirement of “talking to him at the harbormaster’s office” before turning in.
Additionally, a quest is showing “accepted” from him called Azerite for the Alliance that is not in my logs at all. So I can’t abandon it, nor can I technically progress it. I think it’s a quest related to expeditions, but I’m not even sure if people are really doing those anymore, so…
Unsure if these two things are related, but it’s extremely frustrating sitting through terrible dungeon groups just to not be able to turn in my quest. (Especially knowing that I have to do more dungeons to unlock Kul Tirans. I just want my cool druid, dudes. 
)
Also having this problem. Can’t get him to phase into the Harbormaster’s Office. Guess I’ll grind island expeditions to see if that moves him?
Having the same issue.
Same here. I posted on the wowhead page a couple of days ago, and 3 other people have reported the same problem.
Seems to be an issue with 9.0.2.
(I did all the usual - drop quest, reset user interface completely, not reinstall any addons before picking up the quest again. No luck.)
I did the entire thing on Alliance to get the mounts, and it looks as though my last few quests won’t be done in time.
Update: I figured out how to fix this extremely frustrating “bug”. If you can even call it that.
Your character needs to have completed the achievement “A Sound Plan” for Flynn to show up in the Harbormaster’s Office. Meaning you have to do all the Tiragarde Sound storylines for him to even appear here. After hours of running around doing tons of unrelated content to this quest, he’s finally here.
Blizzard, what the hell lol
Thanks for the info, appreciate your taking the trouble, off to Tiragarde it is then. What a pita.
It worked - I finished off ‘A sound plan’ and Flynn appeared in the Harbourmaster’s Office, and I was able to finish the quest. He dithers a bit, but it got done.
Your character needs to have completed the achievement “A Sound Plan” for Flynn to show up in the Harbormaster’s Office. I finish this achievement and he is appear in the office
Confirmed! I had two remaining parts of “A Sound Plan” achievement. Completed those and Flynn appeared in the office.
This is literally true but also bs. Locking 1 quest completion behind 20 unrelated ones is not 5-star game design.
I have a this bug as well but the character in question already has the achievement “A sound Plan.”
I have the same issue and also have completed that achievement.
I tried that. It doesn’t.
You need to do the quest line 'A Sound Plan
Have you completed ‘A Sound Plan’?
Ok adding to Torien’s suggestion which works.
I wanted to add:
the account-wide achievement “A Sound Plan” does NOT count i.e. the character who needs to complete “Tol Dagor: The Fourth Key” and cannot because Flynn is unresponsive must complete the “A Sound Plan” questline, even if you have already completed it on another character, and have the achievement marked as completed.
I’m guessing it’s some sort of phasing issue with Flynn.
This was extremely frustrating to figure out. Every time I tried one of Blizz’s suggestions (none of which worked I might add), I would go to the harbor office and there were usually 3-5 people complaining and baffled as to why they couldn’t interact with Flynn.
What a great way to spend a weekend. Thanks Blizz!