A point worth noting. We've had this issue whenever we had to themes on website with custom sidebars. Our angle for this particular problem was to integrate an importer into our own solution for custom sidebars (Power Widgets). The importer allows you to inherit custom sidebars settings from the old theme and keep them active on the theme, with the ability to match sidebars to inherit old settings - this comes handy whenver themes vary in their default widget areas. The feature explained here: http://goo.gl/QVCuGq Feedback welcome