MKVToolNix can help you with cutting down the DTS tracks. Drop in an MKV file with just the audio you want to cut mixed in, split the file based on frames you want to cut in the “Output” tab, then drop the first portion of the film you chopped up in a new window and append the second portion of the film that you to that file and voilà. No encoding required.
Oh wow thank you. That actually seems remarkably easy.