Yes, the difference in frames is why you can't just rip DVD source and insert it in the scripts where you used the download file without any further work, which I used to think would be possible. It's why you'd need to recut it. I think the difference comes in either the networks cutting off a little for broadcast to mix in the commercials or the uploader/encoders not always cutting at the exact same place when they rip for upload.

The color and crispness shouldn't make a difference in the basic scripting, although you might need effects tweaking. But that's after replacing the files.

So have you remastered anything? How do you approach reclipping?