Index: wp-includes/widgets.php
===================================================================
--- wp-includes/widgets.php	(revision 19341)
+++ wp-includes/widgets.php	(working copy)
@@ -1166,13 +1166,13 @@
 
 	$registered_sidebar_keys = array_keys( $wp_registered_sidebars );
 
+	$orphaned = 0;
+
 	$old_sidebars_widgets = get_theme_mod( 'sidebars_widgets' );
 	if ( is_array( $old_sidebars_widgets ) ) {
 		// time() that sidebars were stored is in $old_sidebars_widgets['time']
 		$_sidebars_widgets = $old_sidebars_widgets['data'];
 		remove_theme_mod( 'sidebars_widgets' );
- 
-		$orphaned = 0;
 
 		foreach ( $_sidebars_widgets as $sidebar => $widgets ) {
 			if ( 'wp_inactive_widgets' == $sidebar || 'orphaned_widgets' == substr( $sidebar, 0, 16 ) )
@@ -1234,7 +1234,6 @@
 	unset($_sidebars_widgets, $_widgets);
 
 	// find hidden/lost multi-widget instances
-	$lost_widgets = array();
 	foreach ( $wp_registered_widgets as $key => $val ) {
 		if ( in_array($key, $shown_widgets, true) )
 			continue;
@@ -1244,10 +1243,10 @@
 		if ( 2 > (int) $number )
 			continue;
 
-		$lost_widgets[] = $key;
+		// Any lost widgets from previous sidebars become orphans, one widget per orphan area.
+		$sidebars_widgets['orphaned_widgets_' . ++$orphaned] = array( $key );
 	}
 
-	$sidebars_widgets['wp_inactive_widgets'] = array_merge($lost_widgets, (array) $sidebars_widgets['wp_inactive_widgets']);
 	wp_set_sidebars_widgets($sidebars_widgets);
 
 	return $sidebars_widgets;