It looks like in your success callback after your ajax call you will need to reinitiate flowplayer by calling
$('.flowplayer').flowplayer();
http://flowplayer.org/docs/setup.html
In addition the "controls" attribute on the video tag doesn't look to be supported by flowplayer. Flowplayer defaults to showing controls and can be removed by using predefined modifier classes on the main div, or hiding them in your css.