A pic of the area would help,but it it's the bottom where the trim meets the hull,Lifeseal is always my choice. It comes in white or black,and stays put,doesn't yellow like other products,and in the same hand it'seasily removable.
If it does become impossible to get the proper molding and it is used to hold the glass in place I'd use the adhesive that they use to glue the windshields into cars. I can't remember what it's called off hand but you can by it off of most automotive jobbers in a calking tube.