I’ve got an mkv where the video goes out of sync with the audio after about 10 minutes. Possibly because the audio had to account for an ad break, there’s a bit of silence that doesn’t exist in the version of the video I’m using.
Is it possible to only delay the audio per chapters for example, so as to only fix the second half?
Unfortunately this isn’t something MKVToolNix offers. It’s simply outside its intended scope.
You’ll have to extract the audio & use some other editor to fix up the middle somehow. Afterwards merge the original file sans its audio track with the fixed audio track into a new file.