if you would like to demux the disc and do a new authoring on that, I would use TSMuxer, as it would not create valid elementary stream.
larry applegate did a lot research on that and tests with eclipse verifier - they all fail.
I would advice to use EasyBD Pro or better, as it has a complete BD-Reauthor-Function.
http://www.dvd-logic.com/easybd/
ok, it´s PC-soft, but it will create 100% valid streams and could handle all that might be on original BD (except BD-j).
you can try/test the application for about 20days at full function.
cheers
danny