If all they did was flip a couple shots could you not remux the stream into an avi and use virtualdub to rearrange the shots (using the copy and paste, possibly cloning or deleting a few frames to make it sync) and import the audio into VD as well as a secondary track to check sync then export it as a direct stream copy? You could then use tsmuxer to remux into whatever container you wish.
I would think so, but I can’t seem to find software that will remux into avi successfully for me. I’m also confused as to how to use the “paste” function in virtualdub…it doesn’t seem to be working.
I thinking it default pastes at the end. Which sucks associated but can still be worked around. Just delete everything after where you need to paste, paste it, then “append” import it again and delete everything in between.
Pain in the ass but might be worth it to avoid reencoding.