Test suggestions
Can you "un merge" them?
What happens if you just link the video and audio (ie. not merge them).
(Does the TC remain correctly in the H264?)
Next what happens if you dont link them but just synch them?
I am assuming you are creaing an EDL for Reconform to Source footage
EDIT:
I can see that wont work afeter testing it.
What surprise me is that the you dont have the TC in the Merged clip.
My test did.
