Don't forget, if just one pass can't be found, the shot is rendered unusable and has to be recreated.
Pardon my ignorance, but if all but one of the passes for a particular model shot cannot be located, couldn't they just recreate the missing pass with CGI?
If it's just the warp engine or deflector pass, that doesn't seem like a big deal. HTV left off certain passes or misaligned them from time to time, and it wasn't a dealbreaker.
One thing to bear in mind is that you're not just talking about painting the nacelle grills blue for each frame (which would be hard enough to do right on a moving object). Those lights interact with the surface of the model in many subtle ways, and trying to recreate that pass in one
frame would be hard, never mind getting dozens of frames to look identical.
I'm not a CG artist, but I think it'd be much easier to just start from scratch.