Well, the opening flash-back has a bald Whitaker, meaning that it most likely was from before the re-shoots (trailers had a bald Whitaker on Jedha as well). And from what Edwards has described it seems that it was Jedha, and mostly Scarif that was re-shot.

There is of course the whole thing about Edwards initially assuming that Disney wouldn’t let them kill off all the main characters, but I don’t know if that only affected the script or if they actually changed the shooting of the Scarif scenes that drastically.