Zero duration subtitles mishandled
If an ASS file contains a line with equal start and end time, muxing it will result in the end time being set to the start time of the next line. This odd behavior will result in previously invisible lines showing up in newly muxed MKVs.
I have older MKV files (e.g. one written by mkvmerge v18.0.0) which contain such zero duration lines, so muxing apparently didn't always have that problem and they are simply ignored by any subtitle renderer. Sadly, zero duration lines are not rare, they are sometimes misused as comments and autogenerated karaoke FX often has them, so ideally they should be muxed as they are.
Here's a minimal ASS sample for testing.
Dialogue: 0,0:00:01.00,0:00:01.00,Default,,0,0,0,,zero length will become
Dialogue: 0,0:00:01.00,0:00:02.00,Default,,0,0,0,,zero length after muxing and demuxing again.