> If they look for scene changes and make new I-frames on scene changes, then we might expect that at least for the scenes that start identically in M1 and M2 they will get identical I-frames and P-frames up to their first edit if any.
> Question: are there any encoders that when encoding M2 to produce C2 can be given M1 and C1 as references using them to adjust I-frame spacing so as make as many C2 I-frames as possible match C1 I-frames?
I suspect if you were to encode both files with x264 with identical settings, in crf mode, with vbv disabled and keyint=0 (unlimited keyframe length), its scene detection should place I-frames in the same places (that is, on scene cuts, not on the timeline). Maybe some scenecut tuning would be necessary.
> That would allow C2 to be stored efficiently as a binary diff from C1. This could be handy if C1 and C2 needed to be checked into a version control system, or you needed to distribute C2 over a low bandwidth or expensive link to someone who already had C1.
I'm not aware of any automated way to do that, but you can do a similar thing manually using mkv's ordered chapters. You first compress the original cut, then you compress any additional scenes and insert them where you need. For example, you can make a mkv file for a theatrical cut of a movie, and then make a separate file for a director's cut that is only as big as the additional scenes are, since it uses the theatrical cut file for the common scenes.