I'm not sure if this information in the first paragraph is pertinent. You may just want to skip to the second paragraph.

So, I got to West Harbor and I received a quest to visit the Dragon Caves and find Tarmas. Went there and found Tarmas being escorted out. Briefly checked out some of the Dragon Caves, not finishing the place. On return to West Harbor found out 'Tarmas' was black dragon in disguise. Beat the black dragon and the people just stand around with the gate remaining locked. This isn't the problem though. I found out I needed to rescue the real Tarmas. Returned to Dragon Caves and found him. On return to West Harbor the gates were opened and all seemed well. I turned in a few quests and picked up some new ones.

Saved my game inside West Harbor, both a big save and a quick save. Came back and loaded the save later and West Harbor is a ghost town except for Quarrel. This would be bad enough except the gate is 'locked'. All i can do is 'look' at it (eye icon when hovering over gate). I don't have a save anywhere near this point. Is there a console command that will allow me to noclip out of the gate or something of that nature? Google searches on NwN 2 cheats come back with cheats that modify variables, stats, etc... nothing involving teleporting or noclipping the player. I figure I'm pretty much screwed out of finishing any quests in West Harbor but I figure I can at least complete the rest of the game... hopefully.

I friggin' hate glitches.

I think KevL over on the Bioware forum is your best bet.

http://forum.bioware.com/forum/45-neverwinter-nights-ii/

[Edit]

Ok... Storm of Zehir. Please ignore.

Luckily I had an autosave that wasn't too old (lost about an hour, which can easily be redone). I immediately went about redoing the black dragon quest in West Harbor, this time returning to the Dragon Cave first to pick up Tarmas. After completing the quests and picking up the new ones I'm able to leave and return with no issue.

Some thoughts...
-I don't think this is some sort of save corruption. Loading both a quick and regular save in town resulted in all characters (except for Quarrel) vanishing.
-I kind of wonder if failing to get Tarmas on the first visit broke a script of some kind. The writing makes it obvious they figured some players might miss him first visit but perhaps the scripting is less solid if he is missed and the Dragons are removed without his presence.
-Perhaps simply West Harbor is buggy and saving in town is risky. I have a save in the world map just outside of West Harbor... I may load it and try doing some quick saves and loads in town to see if I can reproduce this bug.

I've finished NwN 2 OC and Mysteries of Westgate (saving Mask of the Betrayer for last) with no issues but so far I've run into two major issues in Storm of Zehir. The above and another in the Temple of Umberlee where if you save during the music puzzle and then load it breaks it. Storm of Zehir just seems to be a bit fidgity with saves so be cautious and make multiple saves... some advice I plan to follow more closely now.

Other than the bugs I really like Storm of Zehir and feel its a bit underrated. It really feels like a more classic D&D adventure similar to the Icewind Dale series which I also just recently replayed (got the enhanced edition).