Yes that is right, you are going to have to rip the uncut version and then ALL files will sync to it, you can't leave it "as is" because it is in chunks on the BD, I really hate when they do that but I guess they have to because of the censoring in some parts LOL, and you do not have the US Universal version right? so you have the FOX version, so it will work, no doubts, because the HK FOX version is exactly the same.
You could also use Tsmuxer to do this, just open the correct mpls(look at the run time) and demux the video portion(but before you close it, go to the Blu-ray tab and copy and paste the chapters) then once finished, open Tsmuxer again and add the video in that you just demuxed, then the new DTS-HD MA 5.1 track and then add the new DTS-HD MA 2.0 Iso score track, I also added the commentary because it is just hilarious as hell LOL, then go to the Blu-ray tab again, click on custom chapters, then paste back in the chapters from the retail BD, then mux, wallah, a new BD with all the new tracks and the chapters in the same position as the retail, and ALL in 100% sync!
1 more thing though, if you are needing to burn a new BD, and need it to be in BD25 size, then use a KICK ASS program called BD-Rebuilder, it is free, and it will take the new BD you just made and re-encode it to fit an a BD25, it won't take long because it is not that much bigger, and you won't lose any video quality, I see NO difference between my retail and my new.
hope this helps, if you need anymore help, just ask away.
OH, and LOL, that Great Sword is UGLY, I love my Conan Atlantean Sword, and it is real, and really sharp, and really heavy, I have to oil it regularly, my second favorite swords are my Twinkle and Icing Death swords, followed by my Ninja Sword, LOL I love blades!