Just to be clear, the only movie I have ever had audio sync issues with is Independence Day. And to show you what I mean with extracting each segment, see the attached pics.
1. You can get the m2ts file order from the playlist. In this case it is playlist 801. As you can see, the first video segment is 600.m2ts. The 2nd segment is 623.m2ts and so forth. You need to note down this order.
2. You select each segment in CloneBD. As you can see, I have located 600.m2ts and 623.m2ts. You would continue to select all movie segments that you noted down from the playlist.
Now, it was about a year ago that I had done this, so I can't remember if I extracted the audio with the video(s) and muxed together in mkvtoolnix or if I only extracted the video(s) using CloneBD and muxed with the audio track I extraced elsewhere.