Just performed the flapectomy on a factory JCW; I'm wondering why the vacuum line goes into the front of the box and then into some type of cylinder inside, the comes out again and connects to the flap motor on top.

I get the flap motor, but what is it controlling on the inside?

 

The vacuum line doesn't control the flap motor, it powers it. Control is via a ~150Hz 12v signal (same as used in the shift light). Is there wiring to the cylinder that the vacuum line goes into?