Playlist conversion/compression - whatcha got?

[Tampastan]

When ripping a Bluray with MKV how are you compressing mixed up playlists with something like handbrake or wondershare video converter? For example, I ripped Deepwater Horizon with MMkv The files were scrambled, thanks to someone here there was a post of what order they were in. I dragged and dropped them in the correct order in wondershare. When the merge and compression were completed the audio in the movie was desynced and it became worse as the movie went on. The individual files before compression were fine. So, I guess my question is, how can I compress a scrambled playlist into a 4GBish file with no audio sync errors? Ive been compressing with wondershare at h264 or h265, 1080, 6 channel, aac, 8000kbps, everything else auto. Wondershare seems to be great with drag and drop but it's not as thorough as handbrake. Handbrake, to my knowledge, does not have the ability to merge multiply files manually, but will get you outstanding results (more customizing options) for non scrambled blurays. What to do, what to use?

[Woodstock]

Not sure what your question is. MakeMKV is a stand-alone application that knows how to navigate the disk structure. If you select "Open" (the BIG button that looks like a disk that spins while the disk is initially read), you will be offered a menu that lets you select titles to make into MKV files.

The resulting files work fine with handbrake as sources to compress.