Add an options on the attach file dialog to either replace any attachment of the same name or if it needs to be retained for audit clearly mark the old attachment as an old version. Currently, the attachment list doesn't display the date, either JRA-3215 so it's not obvious that you're getting the latest version.

I't also be useful to have an optional automatic comment, like: "Attachment [^xxx.yyy] added/updated 2009.11.11 1237 by Jim Birch"