I had to discover that it is kind of a deal if you want to transcode the audio or want to make subtitles fit. I’ve stumbled on this when I tried to make a stereo audio track (with dialog normalization applied), but it always went out of sync after the break from part 1 to part 2.
But there is a solution which again uses MKVtoolnix.
Use the “Split files” method from the companion post of this one here: [HowTo]: splitting multi-episode files with MKVtoolnix GUI
I used it to remove the over-long silence from the end of part 1.
Which then (after I’ve put the two parts together) allowed me to create my stereo audio track which stays in sync over the whole play time.
