The .flv is never integrated into the swf. You have to upload that video file as well as the swf in order to get the swf to play the flv.
Your flash file generated your player swf, a control bar swf and some html and as_content.js code. Alongside all of that should be your flv file. That also needs to be uploaded to your website. If you had your flv in a folder somewhere else, it's best to bring the fflv file next to the fla document and relink it.
http://www.YouTube.com/ShiveringCactus - Free FX for amateur films