I don't know that I would prune vandas in the winter, but then again they hate me so I probably don't know what I'm talking about.
You can chop the vanda stem directly above the old roots. I've seen this done when there is an aerial root or two forming higher upon the stem that can support the vanda until new roots are growing. The old part with the dead roots might even sprout a keiki from somewhere. If you post a picture I can tell you where to cut