I went through pretty much the entire story quest the other day to test it out.
here are the results.
Everything works fine through the missing kids (with the exception of the monster children not attacking me when they spawned).
Everything in the soul crystal part worked Ok too except that i got no reward at the end.
The fairy appeared and set me off on the mushroom quest which worked fine up to the point where i had to kill infected pomics. They do not spawn when you have this quest and kill regular pomics.
After spawning some of my own i completed the quest and continued the story up to the point where Mairard sends you to Junon Polis. At this point you should get free passage on the boat but you don't.
You also don't get passage back on the boat from JP after picking up the item there.
Finally after delivering the box back to Mairard, he gives you the item in the box but it never goes into your inventory or even tells you that you recieve it. This item should be the Junon Mask.
Then it all ends, normally to be restarted a bit later (level 30 I think) though I don't know if the quest actually went beyond this in pre-evo (incidentally, we should just be able to import the quests from evo shouldn't we?)
The next time I re-logged, the fairy appeared to me and started me on the whole sequence all over again. What's the deal with that? is it just because I am past the end of the quest sequence?