Did you get a preview of the locations of the 4 levers when you entered? Do the levers have a blue glow effect, indicating they have not been disabled yet?
Can you highlight the levers, but nothing happens when you try to use them, or can you not target them at all?
In the Source Square (before entering the courtyard with the engineer) there is a teleporter shrine. Did you try leaving and returning, to get the game to reload the area to see if that would help? Returning to the battle tower would also get the game to reload the area.
In the Developer Mode cheat menu there is a function to open nearby locks and chests. I don't know if that would work with levers, but it couldn't hurt to try.
In the Forgotten Crypt, if you mindread Skulk 3 times you can learn enough of a spell to tell Abbott so he doesn't have to sacrifice himself at the end of the crypt. Whether he lived or died, you could try the opposite, and see if that makes any difference when you get to the levers (if he is alive he keeps the traps in the courtyard disabled).