Replacing switched 14/2 with 14/3
You could leave it in the boxes, capped, or chop it off. The problem with leaving it in the boxes is you may run up against box fill rules. If you do leave wires in the boxes, even temporarily, any wire by itself should generally have a piece of tape over the wire nut and wire insulation to make sure the cap stays on as the caps generally are designed to hold properly with 2 or more wires.