diff --git src/wp-admin/includes/schema.php src/wp-admin/includes/schema.php
index 4f49dc2..f8ffd2a 100644
--- src/wp-admin/includes/schema.php
+++ src/wp-admin/includes/schema.php
@@ -427,6 +427,7 @@ function populate_options() {
 	'comment_moderation' => 0,
 	'moderation_notify' => 1,
 	'permalink_structure' => '',
+	'rewrite_rules' => '',
 	'hack_file' => 0,
 	'blog_charset' => 'UTF-8',
 	'moderation_keys' => '',
diff --git src/wp-includes/class-wp-rewrite.php src/wp-includes/class-wp-rewrite.php
index 035bbc3..01d66f2 100644
--- src/wp-includes/class-wp-rewrite.php
+++ src/wp-includes/class-wp-rewrite.php
@@ -1772,7 +1772,7 @@ class WP_Rewrite {
 			unset( $do_hard_later );
 		}
 
-		delete_option('rewrite_rules');
+		update_option( 'rewrite_rules', '' );
 		$this->wp_rewrite_rules();
 
 		/**
diff --git tests/phpunit/tests/rewrite.php tests/phpunit/tests/rewrite.php
index 1f7426e..5db9edd 100644
--- tests/phpunit/tests/rewrite.php
+++ tests/phpunit/tests/rewrite.php
@@ -320,4 +320,19 @@ class Tests_Rewrite extends WP_UnitTestCase {
 		$this->set_permalink_structure();
 	}
 
+	/**
+	 * @ticket 29107
+	 */
+	public function test_flush_rules_does_not_delete_option() {
+		$this->set_permalink_structure();
+
+		$rewrite_rules = get_option( 'rewrite_rules' );
+		$this->assertSame( '', $rewrite_rules );
+
+		$this->set_permalink_structure( '/%year%/%monthnum%/%day%/%postname%/' );
+
+		$rewrite_rules = get_option( 'rewrite_rules' );
+		$this->assertInternalType( 'array', $rewrite_rules );
+		$this->assertNotEmpty( $rewrite_rules );
+	}
 }