Thanks for your answer Jim, but I think I haven't made myself clear. I'm trying to output a .swf, not a DVD or Blu-ray.
When I'm outputting a DVD or a Blu-ray from Encore I can encode the asssets in Premiere or AME exactly how I want them, and if they're compliant I can bring them into Encore and Encore will not transcode them further. It will build the DVD using exactly those assets and not transcode them further.
I want to do exactly the same thing with Flash files to output a .swf.
I may be misunderstanding how a .swf works, but for sure I don't want to go through unnecessary compression steps. Hence my question about what the best format for exporting from Premiere CC is if I can't prevent Encore from recompressing F4V files.