diff --git a/wp-includes/class-wp-customize-nav-menus.php b/wp-includes/class-wp-customize-nav-menus.php
index 87e95009a3..d178de3e24 100644
--- a/wp-includes/class-wp-customize-nav-menus.php
+++ b/wp-includes/class-wp-customize-nav-menus.php
@@ -529,10 +529,11 @@ final class WP_Customize_Nav_Menus {
 	 * @since 4.3.0
 	 */
 	public function customize_register() {
+		$changeset = $this->manager->unsanitized_post_values();
 
 		// Preview settings for nav menus early so that the sections and controls will be added properly.
 		$nav_menus_setting_ids = array();
-		foreach ( array_keys( $this->manager->unsanitized_post_values() ) as $setting_id ) {
+		foreach ( array_keys( $changeset ) as $setting_id ) {
 			if ( preg_match( '/^(nav_menu_locations|nav_menu|nav_menu_item)\[/', $setting_id ) ) {
 				$nav_menus_setting_ids[] = $setting_id;
 			}
@@ -627,7 +628,7 @@ final class WP_Customize_Nav_Menus {
 			}
 
 			// Override the assigned nav menu location if mapped during previewed theme switch.
-			if ( isset( $mapped_nav_menu_locations[ $location ] ) ) {
+			if ( empty( $changeset[ $setting_id ] ) && isset( $mapped_nav_menu_locations[ $location ] ) ) {
 				$this->manager->set_post_value( $setting_id, $mapped_nav_menu_locations[ $location ] );
 			}
 
diff --git a/wp-includes/theme.php b/wp-includes/theme.php
index a69f4830cc..4e5f63bb8e 100644
--- a/wp-includes/theme.php
+++ b/wp-includes/theme.php
@@ -694,7 +694,7 @@ function switch_theme( $stylesheet ) {
 	}
 
 	$nav_menu_locations = get_theme_mod( 'nav_menu_locations' );
-	add_option( 'theme_switch_menu_locations', $nav_menu_locations );
+	update_option( 'theme_switch_menu_locations', $nav_menu_locations );
 
 	if ( func_num_args() > 1 ) {
 		$stylesheet = func_get_arg( 1 );
@@ -2724,8 +2724,9 @@ function check_theme_switched() {
 	if ( $stylesheet = get_option( 'theme_switched' ) ) {
 		$old_theme = wp_get_theme( $stylesheet );
 
-		// Prevent retrieve_widgets() from running since Customizer already called it up front
+		// Prevent widget & menu mapping from running since Customizer already called it up front
 		if ( get_option( 'theme_switched_via_customizer' ) ) {
+			remove_action( 'after_switch_theme', '_wp_menus_changed' );
 			remove_action( 'after_switch_theme', '_wp_sidebars_changed' );
 			update_option( 'theme_switched_via_customizer', false );
 		}
diff --git a/wp-includes/version.php b/wp-includes/version.php
index b95739da49..bcc51f5d35 100644
--- a/wp-includes/version.php
+++ b/wp-includes/version.php
@@ -4,7 +4,7 @@
  *
  * @global string $wp_version
  */
-$wp_version = '4.9-beta3-41994';
+$wp_version = '4.9-beta3-41995';
 
 /**
  * Holds the WordPress DB revision, increments when changes are made to the WordPress DB schema.