Quests are not always listed in chronological order (like for example Zoltan Gwent quest), so I don't think Ves quest was in any shape or form related to Ebbing plotline. The only other thing I noticed is that Vincent was going to have one more sidequest related to him. It looks like Ebbing's story is composed of four sidequests listed as Wojna (War) and since even Emhyr himself would get involved, it's quite possible this is how originally we had an option to affect final outcome of the war between North and Empire, but of course that's just my speculation, so it doesn't mean it's true.
From the pieces of asssets I gathered the plotline would look like that:
Part 1 (Roche's Gang) Judging by the name, Roche would ask us to find his agent, who actually is Thaler. It's similar to how A Deadly Plot quest plays out in the final game (Thaler is a shoemaker, we find him with the trolls), but there is a large section missing. Geralt follows the trail to the Stone Cutters village, where some kind of massacre happens, there are bodies of dead peasants and Nilfgaardians killed by the plague. Masked man, Martin Krafft Ebbing, seems to have something to do with it, since he serves as the main villain of this plotline. He's accompanied by mutated soldiers and would forcefully inject Geralt with some kind of poison (possibly with virus in order to create antibodies). The whole village would be covered by a mist with the wraiths implying some kind of supernatural powers on Ebbing's part. He definitely seem like a mad scientist type who possibly tested Catriona on the northern peasants, as well as conduct some genetic experiments.
Part 2 (Investigation) Here's where Devil's Pit comes into play. This is also where the misconception of player meeting Iorveth in abandoned house in nonhumans district while playing his flute came out. There is a sound of Iorveth playing the flute from TW2 in SFX section, but it looks like it's just reused SFX asset, similar to how some peasants in the game play the same melody on their flutes, since outside of that there is no mention of him in this whole document, which is one of the most recent ones, that implying he was removed from the game by that point. Now when we finally explained that, let's get back to describing the quest proper. It looks like the first idea for this quest was to start it in nonhuman district where Geralt would find alchemical lab and portal leading probably straight to DP, but they changed it into Geralt following the leads he find in the forest, which is covered in blood and guts. It would turned out it was the way, which Nilfgaardians delivered the bodies of plague victims from field hospital to Devil's Pit, eventually turning it into a mass grave. It looks like it was a part of the Ebbing experiments. The rotting corpses lure the horde of beasts, which start bothering Nilfgaardians. They would try to get rid of them by capturing arachas and using it's venom to keep the monsters away (this is where the flute would come into play I think).
Part 3 (Assassination): Geralt gets taken inside Nilfgaardian camp (though he would be limited to just one tent) where he gets to chat with Nilfgaardian spy and Emhyr himself via Megascope, which means that would be some serious business. In White Orchard, if you give temerian agent into the hands of Nilfgaardians, you can find out about some kind of plague bothering their army. So my guess is that Ebbing was working for them, testing the Catriona virus on northern peasants, with his crimes being covered by war, in order to find the cure for the plague. As you remember, Nilfgaard was the place where the Catriona started (via Ciri), so that would make sense they would be hit with it pretty badly, on top of that with bacteria of unknown origin. Geralt was also going to visit Martin's residence, probably to off him.
Part 4 (Lazaret) This is where everything is being confusing, so I can't tell much about it. The quest takes place in field hospital, full of bodies and plague victims. Ebbing would be dead by that point with his finger missing due to making a pact with some demonic being that is also summoned. Geralt uses Martin's body to make a ritual, possibly to drive demon off. There is some battle going on outside, hard to say between who. Geralt obtains the antidote developed by Ebbing, so I think (again, just my speculations) player would get the choice to give it to Nilfgaardians or not, which would possibly affect the final outcome of the war. That's all I gathered.
