Correct me if I’m wrong, but the work flow was Harmy’s Lossless source, re-encoded to 20-ish gb MKV file (when it became v2.7) and then re-encoded to a more compatible BD format?
You did not use a lossless master?
It was already BD compliant the way I encoded it. IIRC, his discs do not have a re-encoded main feature.