Did you ever manage to finish this?
Yesterday I found out that the nightlies of handbrake support bluray subtitles so I decided to give this another try and combine the 2 parts of each movie into a single mkv. Works very well and it does save quite a bit of storage
.
Basically I ripped the BD's with Anydvd to a folder, I then used TSmuxerGUI to a new bluray folder to strip it from anything I don't need and used the split & cut tab on the first part of each movie to remove the trailing blank. When all 6 are done, I used TSmuxerGUI to join the 2 parts again into a single bluray folder. Finally, handbrake to turn it into an mkv, compress it a bit, passthrough for DTS-MA track and the icing on the cake, keep the subtitles.
I used the highest advised quality settings for the video and enabled film tuning. The first movie shrunk from 59GB to 16GB, 2nd movie shrunk from 60GB to 19GB and 3rd movie is 68GB but still processing, I expect it to end up around 23GB. First two are perfect, no sync issues, playback is good and no visual artifacts whatsoever and the transition from part 1 to part 2 is smooth and invisible.