Hi everyone
BEWARE: Possible spoilers of Hoard of dragon Queen.
I have been DMing since 3.5 and back then I made a lot of reading about the cities and gods of Forgotten Realms. That was done to try to integrate my custom adventures in the existing FR lore, since my players played a lot of Baldur´s Gate and Neverwinter Nights (me also) and wanted to avoid conflicts with the canon.
I skipped the 4ª Edition for various reasons. The most important was that i had spent a lot of money in 3.5 and didn’t want to start all over. I know there was the sundering and spellplague (which i am still clueless about because that lore didn’t appeal to me)
Now I am back running expeditions and encounters (Hoard of dragon queen) in 5.0. My problem is that i haven´t seen no new product or information of what happened in the realms since 3.5. Although i found some information in the internet, some of it is imprecise or of conflicting nature.
At this point we are in chapter 5 and due to players choices and also since i am not very happy with chapter 5 (i think it´s very poorly written) the plotline has made a different turn from the book. The Cult of dragon is smuggling the stolen hoard from Waterdeep by way of the Underdark and not from some silly construction work wagons.
And then it all comes down to Skullport.
I always found the ideia of the dark twin of Waterdeep very appealing and wanted to make a campaign (or part of one ) in Skullport.. Back in 3.5 i saw the city similar to Port Royale or Tortuga back in the Pirates Golden Age in Caribbean.
Something of Frontier town where people would meet and goods and coins would change hands between people and races that normally would attack each other on sight. The ruling authority would come from wealthy merchant and nobles that wish to maintain the situation has calm as possible so that everyone would profit from it. The religious aspect would be maintained by the clergy of Eilistraee (and maybe Waukeen) that would hunt Lolth worshipping drows and similar lawbreakers. At least it was how i used to see it.
But know i have read that Eilistraee was killed in the 4.0 edition and that the cave of Skullport was mostly destroyed and the city abandoned. So now what.... Where do i go from here?
The cult is still going for the Castle in the Mire of Dead Men like in Chapter 6. The underdark was simply the best way to skip unnoticed from spies and thiefs.
My option are:
A) I could make the players explore the ruins of Skullport while searching for the cult of dragon.
B) Ignore official Lore and make the city has it was, ignoring 4.0 editio,
C) Ask for advice from fellow DMs in D&D Foruns 
Thanks in advance for you time and help
Umbacano.
P.S: What happened to Gemna Silverstonte (The Zhent gnome assassin in Chapter 4)? I don’t see her anywhere in the rest of the book.
Most of what happened during the 4e era has been changed back to how it was before during the Sundering. No one knows the full extent of the changes or what the current state of most of the Realms is, though, because Wizards ain't sayin'.
During the playtest period, they made this big fuss about how Encounters players could "shape the future of the Realms" by reporting their progress in the various Sundering adventures, but there's been no word as to what that future looks like. All we have to go on is the limited info they've provided us with in Lost Mine of Phandelver and the Tyranny of Dragons adventures (both the two main modules and the smaller Adventurer's League ones set in and around Phlan). It's getting to be a little frustrating.
There's been some speculation that they'll give us something at Gen Con, but that's still months away. It'd be nice if, in the meantime, they let Ed give us some updates via his old website column.
Anyway, I'd suggest Option D: Doing what is easiest and most fun for you and your group. If that means accepting that some gods are dead and Skullport is in ruins, then do that. If it means ignoring all that stuff and having Skullport still be a thriving pirate haven, then do that!
There is no reason the Cult didn't excavate the tunnel if they where planning on using it. They have a lot of gold and members. Maybe the party to run into a group of dwarven miners that escaped with their lives after it was finished when the Cult tired to murder everyone involved which is the lead the PCs need.
Alter your games timeline. That is what I did. So, following FR canon lore, v.3x lasts from DR 1372-1376. The Spell Plague begins in DR 1385, and v.4 begins after the SP stabalizes in DR 1479. Version 5.0 begins in DR 1489.
I am like the OP, and didn't care for the storyline beginning with the Spell Plague. So, in my current campaign, the year is DR 1372, and we are using v.5 rules for it. I get to use the new crunch, with the fluff I like. Best of both worlds. I believe both of the starting modules for v.5 can easily fit into an older timeline.
Thanks for all the help and advice. I wiil take those into account and try to find a proper solution.