Actually, 99% sure that the answer is no.
A few quests were removed with the update. But these quests still show as uncompleted in your log. Even if you already did them.
(Only reason why I'm not 100% sure is because I haven't checked if those are the same quests as the ones you are missing. I'm lazy like that. )
Oh yes, I'd forgotten they removed some of those quests... In which case I suppose the answer is no, but also of little consequence.
Just really annoying that they show up, for those of us "MUST GET ALL QUESTS!" OCD people :p
One of the GM's said they will be removing them from our quest logs with a future patch. I would prefer to have them and that whole storyline back.
Why? It's the island of dawn story line quest and the change is unnoticeable. The main story is still told without them.
I think you guys are sentimental. ;P
I tried out the "new" Island of Dawn its much faster to level up and leave the place. I tried it out with 5 character with different classes and on average, it takes about 45 minutes to complete the entire island and reach lv 12.