Yes. When you extracted them, you expanded the channel within the rubber piece.
I use channel lock pliers to GENTLY compress the channel back down until it is almost closed along the entire length of the strip.
Then I use a wooden mallet to seat them.
BE CAREFUL OF HITTING THE SWITCH ON THE PASSENGER SIDE !!!!!

You must be the king lurker on here - member for 6 years and only 2 posts.