Maybe I'm missing the point here, but at least during the scenes I already stated, it should actually pretty easy to distinguish between what is considered to be derived from the CDS master and the new mix.

Furthermore, I would start my investigation by decoding the files to PCM and compare the channels individually also visually in a wave editor. Even any level or dynamic differences would be interesting since the small differences caused by the different formats (AC3 vs. DTS) won't introduce them if decoded properly.