I basically stored the contents of the DOM element that holds the player element in jQuery data on DOM ready:
$('.video-holder').each(function(i,el){
$(el).data('init-state', $(el).html());
});
... then reset the contents (thereby detaching the Flowplayer instance) by calling the stored data back into the holder element's HTML to effectively 'reset' it:
$('.video-holder').each(function(i,el){
$(el).html($(el).data('init-state'));
});
I've only tried this using Flowplayer manual setup, don't think it'd work on auto. Also it probably wouldn't be great performance-wise if you were doing it over and over as the original Flowplayer instance is still loaded in memory, just detached, but was the best solution I could come up with.