What kind of darkening does your scanner do? What needs to be changed is not the brightness/contrast, but the exposure. Changing brightness/contrast means the scanner scans the picture in as normal and adjusts it after it finishes scanning. Lowering the exposure means the scanner scans with a bit less light, which is what you need.
The reason for this is because pencil is reflective. It makes the light from the scanner bounce right back into the scanner, and the scanner thinks that area is white, or at least lighter than it should be. Lowering the light the scanner gives off should lower the amount of light the pencil lead on the paper reflects away.
Another thing you can do, if your scanner can't change its exposure, is to go over the pencil drawing with pen, then erase the penciling. Pen ink still reflects, but only if it's fresh. Once all the water dries away, the scanner can pick it up just fine.