Ok, where to start. First, I hope this hasn't been submitted yet, I didn't see it in the master list of bugs thread.
Where I'm at in my game (PC from Steam):
I have recruited Nalia and done (some of?) her quest. It looks "complete", but who knows, I've never used her or done her quests before. I sprung her from jail and got her forced fiance arrested for jackbaggery.
I've recruited Neera, but done very little with her quests/story other than just having her blow stuff up (including me sometimes).
I have "joined" the Shadow Thieves through Gaelen, by paying the discounted rate of $15,000. I did the dock supervision quest for the thieves, in addition to interrupting (and killing) the recruiter who's stealing his members.
On the way to the current leg of the quest, namely investigating the graveyard, I decided to do the ghost with a missing teddy bear subquest. That of course required me to poke around the back of the Copper Coronet looking for her murderer, and while I was there I decided to free the slaves, too.
Hendak (the gladiator guy who takes over the Coronet) asked me to clear the Slaver Stockade, so I did that too, via the entrance in the sewers.
Now, every time I leave the slaver area (by either the main door, or back through the sewers), Act 3 and/or the city and/or my whole game gets rolled back.
Obviously I'm not missing any loot or XP or anything, just everything is undone.
Walking outside triggers the initial Gaelen offer for $20,000 and I get dragged back to his house and see the chapter begins cutscene for "The Deal is Made!". The guards in the Copper Coronet are still alive (and hostile, despite welcoming me to the Coronet during sword swings), and people who flag me down for conversations/quests are all back and doing all that over again. Hendak isn't the proprietor of the Copper Coronet, the sleazeball guy is, and Hendak's back in the cell. Freeing Hendak a second time appears to result in nobody owning the Coronet (unless he's hiding/lurking somewhere).
Thankfully, I also have the game on my iPad, and the last time I saved was right before all this happened (Hendak was saved but I hadn't gone to the slaver base). I just iFunbox'ed it all back, and will set the slave base quest aside until patched.