Flash HD? From a Video source??? Not worth it IMHO. The kind of system that it would take to play that back would have to be a very powerful system. Flash has a difficult time playing back well at even 640x480, so imagine the issues with content at three and half times that resolution is going to do.
With that said, there is a difference in having a Flash video that is 555x312 natively, and then is scaled to full screen by the player. This would be much safer. To get this encoded in high quality, you would need to use the On2 encoder. Telestream Episode (formerly Popwire Compression Master) has an excellent implementation of the codec for an additional fee.