Currently, Community deletes closed questions with downvotes as part of a self-cleaning measure. The problem is that we generally don't want to delete duplicates, as they improve searching, increase hits to the site, and whiten your teeth while you sleep.
My proposal is to change Community's behavior so that he only deletes closed, downvoted questions if they were closed for reasons other than "duplicate".
For what it's worth, this issue was raised because of Community's deletion of this question on Academia.SE (10K only).