If I'm not mistaken, that part is part of the hinge, I think there are two of them on the hinged side of the walk through window. I think if you slide both of those plastic things a certain direction it enables you to totally remove the pass through window. I have the same thing on my Lund.
I tried contacting Water Bonnet regarding a vinyl top I have. You need to look a bit, but get on their website, find something that says "contact us" which will be an email address. Include a picture of your part in your email.
They got back to me in a day or two.