I would never edit using the original codec of a Blu-ray or DVD as it can cause a lot of problems. I always convert the video to lossless avi using the lagarith codec.
I won't be using any deleted scenes off the blu-ray for ESB:R no matter what scenes it may contain because for one it won't be out in time and secondly i really don't think ESB needs anything added and the SE is a good example of that. ROTJ:R may be a different matter altogether though