Oh that's unfortunate! In my experience it depends on how long you left the chain resting on the leather. Not the same thing, but I've forgotten to store my WOC properly and the zipper made a new dent in the leather quilt that just won't go away. Hopefully your quilts will plump back up a bit, but I'm not sure if they'll ever go back to 100%.
They may pop out depending on how deep they are and how long you've stored your bag like that. I had a dent that I eventually popped back out. I "massaged" the area gently every once in a while but don't know if that aided the process. Can you post a picture?