Unused Items *spoilers*

[Bourlingueur]

The same thing happened to me with the wooden crank on my first playthrough, however...

In the control room before entering the sewers, there is a door that you have to lift by turning a valve. Once you complete all puzzles in the area and try to turn the valve again, it will break and you will have to use the crank instead. It didn't happen on my first playthrough though, so I kept the crank until the end while wondering what it was supposed to be used for.