I think I screwed up.
Got all the reagents, added them to the apparatus and placed the chemistry pot beneath to collect the acid.
Then went back to the main hall, went down the stairs and burned away the organic stuff.
So then I though, "what if I need more acid later on?" and went back to the lab so I would have some with me. Unfortunately, the pot no longer works with the apparatus. So be it, I thought and went back to the hall.
Only now, the organic material is back and I have no acid. And no way of getting any. And no way of proceeding with the game.
Has anyone else come across this?
You may have hit a bug. I think the dev's expected the player to move on to the next section after getting rid of the organ thing. See if the game made a save after the organ.
I think another player had this problem in the official frictionalgames forum.
Money is Humanity.
I'm such a noob. Didn't even realise the game had saves :/