the blu-ray is main video source. the theatrical cut scenes will be taken from the hd broadcast. if possible i try to keep the video untouched as much as possible. meaning no re-encode for the most part of the movie. only the re-inserted theatrical scenes would be encoded to vc-1 and then joined.
there are options to do this, which will be tested upfront. if i can't get it to work, the whole movie will be re-encoded to avc.