You could try this:
make a copy of the timeline with your chapter marks and remove everything from this timeline. Put a long black clip into it and process this through BitVice. I think it should process quite fast, but maybe not. If yes, then import this m2v file into DVDSP, drop it on a track and the chapter marks will be placed correctly. Then remove the black clip and place your encoded video ont the track.
The other way would be to extract the markers from the new m2v file with a Hex editor and to copy it into a copy of the “old” m2v. Not that I really would try that under a deadline…