I use Audacity for this. I load both files, look for a peak or end of silence in both. The difference I remux with Mkvtoolnix. I do this with 2-3 spots. Loadi

I use Audacity for this. I load both files, look for a peak or end of silence in both. The difference I remux with Mkvtoolnix. I do this with 2-3 spots. Loading the file is usually the longest waiting period.