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.