Would you use the English theatrical stereo DTS-HD MA track from Harmy’s, then? I don’t recall if you had this problem, but I needed to swap it in with multi-avchd rather than the software you’re using. Problem is (for me) that multi didn’t place nice with branching titles.
Yes. I just used EAC3To to extract the lossless track from the DTS-HD MA as a .wav, then using VirtualDub I loaded the SSE video and Audio -> Audio From Another File… selected the new .wav. Edited the footage to End of flyover, File -> Save as Wav; revert edits and this time edit for the rest of the film and save .wav. Then simply refresh the assets in the authoring software and boom, New English Stereo Audio track to replace the old glitchy one.
If I needed to, I could re-encode as DTS-HD and then bring that in, but PCM is fine for this disc.