After removing the windshield, any excess glue, etc. should be removed or trimmed away, scratches primed to prevent rust, and prepped for the new clips. In the case of this 2011 Honda Pilot, new moldings and clips were obtained and the clips were adhered in alignment.
Once the new windshield was installed, the new side moldings were easily snapped back into place. Once again, this vehicle looks like a million bucks. Many "installers" don't know (or care) how to remove them properly, and figure the customer won't notice the difference anyhow. Well the customer of this vehicle did, fortunately for him.