Help with removing roof rail covers!

I just removed the roof rails yesterday with ease....but there is still a problem. When removing the rails, the rubber seal attached to the rails kind of pulled the roof molding out of place with the middle strip sticking out rather than being flushed. Should this be a concern? If no rust or mold will grow under the molding, then I could just leave it alone....or should I remove the strip and re-install?
 
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