Hi Stan,
I've tried my best to see if I can get Encore not to transcode a flash file, but I think that, since there's no flash preset (unlike the DVD and Blu-ray presets), I just can't fool it.
However, here's my workaround: I output the flash file any old way: using the DVD or Blu-ray assets, whatever. And then in the output directory it creates I can replace its created assets (in the sources folder) with my own simply by renaming and replacing my own encoded assets with the ones Encore created for me. There's a visible quality improvement doing it this way, and no unnecessary re-encoding.
Of course this is all a bit old-hat anyhow as we'll be doing it the HTML5 way with some Edge program or another any minute now! But for the moment....
Thanks for your help and suggestions!
Cheers
Mark