If you are lucky enough to come across a Ford flex that either hasn't been done before, or has been done by someone who knows what they are doing, then good for you! If not, then be prepared to obtain new moldings from the local Ford dealership. The following video is basically explaining how to remove the side moldings so that when you put them back on, they will snap back into place as they should. (Basically, break the top guide peg so that you can slide the molding from the clips.)
Once the side molding is removed, you'll notice that the clips remain on the vehicle frame.
Twist the clip a quarter turn, then pull the clip. It should release with ease. Slide the clips ack into the sde molding, then line the holes with ht3e clips and snap back into place.