OK. I made the test. The bad flush_rewrite_rules( false ); is present two times at line 616 and line 638 in functions.php. I commented these 2 lines, then went back to settings->permalinks, clicked on 'save changes' and my pages are back.
Please send to the theme author this link: http://codex.wordpress.org/Function_Reference/flush_rewrite_rules#Usage which clearly states that using this function in an 'init' hook is bad practice.