I demuxed the video to an ac3 audio file and a .m2v file, which I'm editing in Premiere. It's my understanding that it's possible to then remux that video file back into the dvd structure while keeping the menus. However, if the video file is a different length, I can see that causing issues, hence the initial question.
My guess is that if there is some way to modify the cell structure, it would have to be in a separate step either before or after the replacement of the new video file.