Alas, after some extensive testing, it's not going to be easy at all. The change takes place in the first vob in the titleset. I took the first vob in the new version and overwrote the first vob in the old titleset and played. It's almost perfect, but you can see a frame jump where the first vob transitions to the second, so this would be robbing Peter to pay Paul.

Two solutions (both of which could be used):
Re-upload the entire torrent and send fresh copies into the pyramid.
Send the AC3, chapter stops, subtitle file, and DVD-Lab Pro files to rebuilt it yourself.

Thoughts?